Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia

Aim Increasing our understanding of the effects of the Last Glacial Maximum (LGM) and determining the location of refugia requires studies on widely distributed species with dense sampling of populations. We have reconstructed the biogeographic history of Clitarchus hookeri (White), a widespread species of New Zealand stick insect that exhibits geographic parthenogenesis, using phylogeographic analysis and ecological niche modelling. Location New Zealand. Methods We used DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene to reconstruct phylogenetic relationships among haplotypes from C. hookeri and two undescribed Clitarchus species. We also used distribution data from our own field surveys and museum records to reconstruct the geographic distribution of C. hookeri during the present and the LGM, using ecological niche modelling. Results The ecological niche models showed that the geographic distribution of C. hookeri has expanded dramatically since the LGM. Our model predicted large areas of suitable LGM habitat in upper North Island, and small patches along the east coast of South Island. The phylogeographic analysis shows that populations in the northern half of North Island contain much higher levels of genetic variation than those from southern North Island and South Island, and is congruent with the ecological niche model. The distribution of bisexual populations is also non-random, with males completely absent from South Island and very rare in southern North Island. Main conclusions During the LGM C. hookeri was most likely restricted to several refugia in upper North Island and one or more smaller refugia along the east coast of South Island. The unisexual populations predominate in post-glacial landscapes and are clearly favoured in the recolonization of such areas. Our study exemplifies the utility of integrating ecological niche modelling and phylogeographic analysis.     

Phylogeography and ecological niche modelling implicate coastal refugia and trans‐alpine dispersal of a New Zealand fungus beetle

The Last Glacial Maximum (LGM) severely restricted forest ecosystems on New Zealand’s South Island, but the extent of LGM distribution for forest species is still poorly understood. We used mitochondrial DNA phylogeography (COI) and ecological niche modelling (ENM) to identify LGM refugia for the mycophagous beetle Agyrtodes labralis (Leiodidae), a forest edge species widely distributed in the South Island. Both the phylogenetic analyses and the ENM indicate that A. labralis refuged in Kaikoura, Nelson, and along much of the South Island’s west coast. Phylogeography of this species indicates that recolonization of the largely deforested east and southeast South Island occurred in a west–east direction, with populations moving through the Southern Alps, and that the northern refugia participated little in interglacial population expansion. This contradicts published studies of other New Zealand species, in which recolonization occurs in a north–south fashion from many of the same refugia.     

Glacial refugia in a maritime temperate climate: Cicada (Kikihia subalpina) mtDNA phylogeography in New Zealand

Understanding the biological significance of Pleistocene glaciations requires knowledge of the nature and extent of habitat refugia during glacial maxima. An opportunity to examine evidence of glacial forest refugia in a maritime, Southern Hemisphere setting is found in New Zealand, where the extent of Pleistocene forests remains controversial. We used the mitochondrial phylogeography of a forest-edge cicada ( Kikihia subalpina ) to test the hypothesis that populations of this species survived throughout South Island during the Last Glacial Maximum. We also compared mitochondrial DNA phylogeographic patterns with male song patterns that suggest allopatric divergence across Cook Strait. Cytochrome oxidase I and II sequences were analyzed using network analysis, maximum-likelihood phylogenetic estimation, Bayesian dating and Bayesian skyline plots. K. subalpina haplotypes from North Island and South Island form monophyletic clades that are concordant with song patterns. Song divergence corresponds to approximately 2% genetic divergence, and Bayesian dating suggests that the North Island and South Island population-lineages became isolated around 761 000 years bp . Almost all South Island genetic variation is found in the north of the island, consistent with refugia in Marlborough Sounds, central Nelson and northwest Nelson. All central and southern South Island and Stewart Island haplotypes are extremely similar to northern South Island haplotypes, a 'northern richness/southern purity' pattern that mirrors genetic patterns observed in many Northern Hemisphere taxa. Proposed southern South Island forest habitat fragments may have been too small to sustain populations of K. subalpina , and/or they may have harboured ecological communities with no modern-day analogues.     

The demographic history of the New Zealand short-tailed bat Mystacina tuberculata inferred from modified control region sequences

Short-tailed bats Mystacina tuberculata were widespread throughout the forest that dominated prehuman New Zealand, but extensive deforestation has restricted them to scattered populations in forest fragments. In a previous study, the species' intraspecific phylogeny was investigated using multiple mitochondrial gene sequences. Six phylogroups were identified with estimated divergences of 0.93-0.68 Ma. In the current study, the phylogeographical structure and demographic history of the phylogroups were investigated using control region sequences modified by removing homoplasic sites. Phylogeographical structure in the North Island was generally consistent with an isolation-by-distance dispersal model. Coalescent-based analyses (i.e. mismatch distributions, skyline plots, lineage dispersal analysis and nested clade analysis) indicated that the three phylogroups found in central and southern North Island expanded before the last glacial maximum, presumably during interstadials when Nothofagus forest was most extensive. Genetic structure within a central North Island hybrid zone was consistent with range expansion from separate refugia following reforestation after catastrophic volcanic eruptions. Phylogeographical structure in the South Island was consistent with southern populations originating during rapid southward range expansion from refugia in northern South Island following postglacial reforestation of the South Island 10-9 kya.     

Extensive genetic differentiation in Gobiomorphus breviceps from New Zealand

Partial mitochondrial DNA sequences for parts of the cytochrome b gene and control region were obtained for 89 upland bullies Gobiomorphus breviceps from 19 catchments in New Zealand. There were two highly distinctive mtDNA clades: a northern clade corresponding to the North Island, northern South Island and west coast South Island, and a south‐east clade, in the southern and eastern South Island. Within these major clades there were further distinct clades that correlated with geographic sub‐regions and catchments. The marked genetic differentiation has occurred in the absence of obvious morphological divergence. Based on cytochrome b sequence divergences and the molecular clock hypothesis, the northern and southeastern clades correspond with the uplift of the Southern Alps during the Pliocene, while populations in the North Island and northern South Island were estimated to have diverged during the Pleistocene. The widescale geographic divergences were similar to those observed in the galaxiids, Galaxias vulgaris and Galaxias divergens , but biogeographic management boundaries may not be the same, reflecting different evolutionary histories for non‐diadromous species occupying the same areas.     

Population structure within an alpine archipelago: strong signature of past climate change in the New Zealand rock wren (Xenicus gilviventris)

Naturally subdivided populations such as those occupying high‐altitude habitat patches of the ‘alpine archipelago’ can provide significant insight into past biogeographical change and serve as useful models for predicting future responses to anthropogenic climate change. Among New Zealand's alpine taxa, phylogenetic studies support two major radiations: the first correlating with geological forces (Pliocene uplift) and the second with climatic processes (Pleistocene glaciations). The rock wren (Xenicus gilviventris) is a threatened alpine passerine belonging to the endemic New Zealand wren family (Acanthisittidae). Rock wren constitute a widespread, naturally fragmented population, occurring in patches of suitable habitat over c. 900 m in altitude throughout the length of the South Island, New Zealand. We investigated the relative role of historical geological versus climatic processes in shaping the genetic structure of rock wren (N = 134) throughout their range. Using microsatellites combined with nuclear and mtDNA sequence data, we identify a deep north–south divergence in rock wren (3.7 ± 0.5% at cytochrome b) consistent with the glacial refugia hypothesis whereby populations were restricted in isolated refugia during the Pleistocene c. 2 Ma. This is the first study of an alpine vertebrate to test and provide strong evidence for the glacial refugia hypothesis as an explanation for the low endemicity central zone known as the biotic ‘gap’ in the South Island of New Zealand.     

Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand

Cook Strait, which separates the North and South Island of New Zealand, has been a transient, but re-occurring feature of the New Zealand land mass throughout the Pleistocene, maintaining its current width and depth for the past 5000 years. Historic land fragmentation coupled with the complex hydrography of the Greater Cook Strait region has created both biogeographic and phylogeographic disjunctions between the North and South Island in several marine species. Here we use mitochondrial cytochrome b DNA sequences of three endemic intertidal limpets, Cellana ornata, Cellana radians and Cellana flava to assess intraspecific phylogeographic patterns across Cook Strait and to look for interspecific concordance of ecological and evolutionary processes among closely related taxa. We sequenced 328-359 bp in 85-321 individuals from 8-31 populations spanning the biogeographic range of the three species. Intraspecific phylogeographic analyses show moderate to strong genetic discontinuity among North and South Island populations due to allopatric fragmentation. This pattern was broadly concordant across the three species and the observed divergence among this group of intertidal limpets (0.3-2.0%) is similar to that of previously studied subtidal organisms. For each species, divergence time calculations suggest contemporary North and South Island lineages diverged from their respective most recent common ancestor approximately 200 000 to 300 000 years before present (bp), significantly earlier than previous estimates in other coastal marine taxa that arose from a miscalculation of divergence time.     

Phylogeographic evidence for two mesic refugia in a biodiversity hotspot

Phylogeographic studies of flora in species-rich south-western Australia point to complex evolutionary histories, reflecting patterns of persistence and resilience to climatic changes during the Pleistocene. We asked whether coastal areas of the mid-west and south, as well as granite outcrops and inland ranges, have acted as major refugia within this region during Pleistocene climatic fluctuations by analysing phylogeographic patterns in the shrub Calothamnus quadrifidus R.Br. (Myrtaceae). We determined variation in chloroplast DNA data for 41 populations across the geographic range. Relationships and major clades were resolved using parsimony and Bayesian analyses. We tested for demographic and spatial expansion of the major clades and estimated clade divergence dates using an uncorrelated, lognormal relaxed clock based on two conservative chloroplast mutation rates. Two distinct phylogeographic clades were identified showing divergence during the Pleistocene, consistent with other phylogeographic studies of south-west Australian flora, emphasising the impact of climatic oscillations in driving divergence in this landscape. The southern clade was more diverse, having higher haplotype diversity and greater genetic structure, while the northern clade showed evidence of fluctuation in population size. Regions of high haplotype diversity with adjacent areas of low diversity observed in each clade indicated the locations of two coastal refugia: one on the south coast and another along the mid-west coast. This is the first evidence for major Pleistocene refugia using chloroplast genetic data in a common, widespread species from this region.     

Phylogeography reveals a North Island range extension for New Zealand's only sexually wing-dimorphic stonefly (Stenoperla helsoni)

Stenoperla helsoni is an endemic New Zealand stonefly characterised by distinctive sexually dimorphic wing loss. Previous distribution records indicated that this species was restricted to the South Island's Southern Alps, although our recent collections of wing-reduced specimens from a site in the Tararua Ranges suggest that this species may extend into the lower North Island. We amplified the mitochondrial COI gene to confirm the identity of North Island specimens, and to assess phylogeographic structuring within the species and genus. North Island specimens were confirmed as S. helsoni, indicating that this species has a much wider geographic range than previously thought. This broad distribution, combined with low levels of intraspecific divergence, suggests that female S. helsoni may be strong fliers, despite males being flightless. Distinct North Island and South Island populations were identified, with a 1.5% divergence between the two populations.     

Comparative phylogeography of three skink species (Oligosoma moco, O. smithi, O. suteri; Reptilia: Scincidae) in northeastern New Zealand

Sea-level fluctuations during the Pliocene and Pleistocene have shaped the landscape of the Northland region of New Zealand. We examined the comparative phylogeography of three skink species (Oligosoma moco, O. smithi, O. suteri) in northeastern New Zealand in order to investigate the impact of the historical processes that have prevailed since the Pliocene on the Northland fauna. O. moco, O. smithi and O. suteri have similar distributions across northeastern New Zealand, frequently occurring in sympatry. We obtained sequence data from across the entire range of each species, targeting the ND2 mitochondrial gene. Using Neighbor-Joining, Maximum likelihood and Bayesian methods, our analysis revealed contrasting phylogeographic patterns in each species. We found substantial phylogeographic structure within O. moco, with three distinct clades identified. Similarly, deep phylogeographic divergence was evident within O. smithi, with three distinct clades present. Clade 1 included O. smithi populations from the Three Kings Islands and the western coastline of Northland, while Clade 2 encompassed the remainder of the range. However, since Clade 3 corresponded to a described species (O. microlepis), O. smithi might represent a species complex. In both O. moco and O. smithi, divergences among clades are estimated to have occurred in the Pliocene, with divergences within clades occurring during the Pleistocene. In contrast, genetic divergence among O. suteri populations was extremely limited and indicative of more recent divergences during the Pleistocene. The lack of phylogeographic structure in O. suteri might be a consequence of its oviparous reproductive mode, which restricted its distribution to warm northern refugia during glacial maxima. Differences in the ecology and biology of each species might have produced contrasting responses to the same historical processes, and ultimately diverse phylogeographic patterns. Our study reveals an absence of consistent and concordant phylogeographic patterns in the Northland biota, even within the same taxonomic group.     

Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum

Aim To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira–Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene‐based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions.     

Multiple glacial refugia for cool‐temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool‐temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial–interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high‐latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.     

PHYLOGEOGRAPHIC PATTERNS INDICATE TRANSATLANTIC MIGRATION FROM EUROPE TO NORTH AMERICA IN THE RED SEAWEED CHONDRUS CRISPUS (GIGARTINALES,RHODOPHYTA)1

Inferring how the Pleistocene climate oscillations have repopulated the extant population structure of Chondrus crispus Stackh. in the North Atlantic Ocean is important both for our understanding of the glacial episode promoting diversification and for the conservation and development of marine organisms. C. crispus is an ecologically and commercially important red seaweed with broad distributions in the North Atlantic. Here, we employed both partial mtDNA Cox1 and nrDNA internal transcribed spacer region 2 (ITS2) sequences to explore the genetic structure of 17 C. crispus populations from this area. Twenty‐eight and 30 haplotypes were inferred from these two markers, respectively. Analysis of molecular variance (AMOVA) and of the population statistic Φ_ST not only revealed significant genetic structure within C. crispus populations but also detected significant levels of genetic subdivision among and within populations in the North Atlantic. On the basis of high haplotype diversity and the presence of endemic haplotypes, we postulate that C. crispus had survived in Pleistocene glacial refugia in the northeast Atlantic, such as the English Channel and the northwestern Iberian Peninsula. We also hypothesize that C. crispus from the English Channel refugium repopulated most of northeastern Europe and recolonized northeastern North America in the Late Pleistocene. The observed phylogeographic pattern of C. crispus populations is in agreement with a scenario in which severe Quaternary glaciations influenced the genetic structure of North Atlantic marine organisms with contiguous population expansion and locally restricted gene flow coupled with a transatlantic dispersal in the Late Pleistocene.     

Fire and ice: volcanic and glacial impacts on the phylogeography of the New Zealand forest fern Asplenium hookerianum

In the Southern Hemisphere there has been little phylogeographical investigation of forest refugia sites during the last glacial. Hooker's spleenwort, Asplenium hookerianum, is a fern that is found throughout New Zealand. It is strongly associated with forest and is a proxy for the survival of woody vegetation during the last glacial maximum. DNA sequence data from the chloroplast trnL-trnF locus were obtained from 242 samples, including c. 10 individuals from each of 21 focal populations. Most populations contained multiple, and in many cases unique, haplotypes, including those neighbouring formerly glaciated areas, while the predominant inference from nested clade analysis was restricted gene flow with isolation by distance. These results suggest that A. hookerianum survived the last glacial maximum in widespread populations of sufficient size to retain the observed phylogeography, and therefore that the sheltering woody vegetation must have been similarly abundant. This is consistent with palynological interpretations for the survival in New Zealand of thermophilous forest species at considerably smaller distances from the ice sheets than recorded for the Northern Hemisphere. Eastern and central North Island populations of A. hookerianum were characterized by a different subset of haplotypes to populations from the remainder of the country. A similar east-west phylogeographical pattern has been detected in a diverse array of taxa, and has previously been attributed to recurrent vulcanism in the central North Island.     

Phylogeographic history of the New Zealand stick insect Niveaphasma annulata (Phasmatodea) estimated from mitochondrial and nuclear loci

We have assessed the utility of a single-copy nuclear locus and mitochondrial DNA (mtDNA) in a phylogeographic study of the New Zealand stick insect Niveaphasma annulata (Hutton). We amplified sequences from the mitochondrial cytochrome oxidase subunit I (COI) gene and the single-copy nuclear gene elongation factor-1α (EF1α) from 97 individuals. Allelic phase at the EF1α locus was determined using Denaturing Gradient Gel Electrophoresis. Phylogenetic analyses showed broad congruence between the geographic distribution of three major COI clades and EF1α alleles, which suggested that the phylogenetic patterns reflect population history rather than lineage sorting. However, the geographic boundaries of these clades were not always in exact agreement between the two loci. Our data indicate that Niveaphasma annulata was most likely separated into a number of refugia during Pleistocene glacial advances. Subsequent to glacial retreat these refugial populations have expanded and now form a number of zones of secondary contact. We contrast these patterns with those observed from other New Zealand taxa. Our study offers compelling evidence for the use of nuclear genes alongside mtDNA for future phylogeographic studies.     

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.     

Glacial refugia and the phylogeography of Steller's sea lion (Eumatopias jubatus) in the North Pacific

Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's sea lions (Eumetopias jubatus) in relation to the presence of Plio-Pleistocene insular refugia. Cytochrome b and control region sequences from 336 Steller's sea lions reveal phylogenetic lineages associated with continental refugia south of the ice sheets in North America and Eurasia. Phylogenetic analysis suggests the genetic structure of E. jubatus is the result of Pleistocene glacial geology, which caused the elimination and subsequent reappearance of suitable rookery habitat during glacial and interglacial periods. The cyclic nature of geological change produced a series of independent population expansions, contractions and isolations that had analogous results on Steller's sea lions and other marine and terrestrial species. Our data show evidence of four glacial refugia in which populations of Steller's sea lions diverged. These events occurred from approximately 60,000 to 180,000 years BP and thus preceded the last glacial maximum.     

Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia

Aim Glacial refugia during the Pleistocene had major impacts on the levels and spatial apportionment of genetic diversity of species in northern latitude ecosystems. We characterized patterns of population subdivision, and tested hypotheses associated with locations of potential Pleistocene refugia and the relative contribution of these refugia to the post‐glacial colonization of North America and Scandinavia by common eiders (Somateria mollissima). Specifically, we evaluated localities hypothesized as ice‐free areas or glacial refugia for other Arctic vertebrates, including Beringia, the High Arctic Canadian Archipelago, Newfoundland Bank, Spitsbergen Bank and north‐west Norway. Location Alaska, Canada, Norway and Sweden. Methods Molecular data from 12 microsatellite loci, the mitochondrial DNA (mtDNA) control region, and two nuclear introns were collected and analysed for 15 populations of common eiders (n = 716) breeding throughout North America and Scandinavia. Population genetic structure, historical population fluctuations and gene flow were inferred using F‐statistics, analyses of molecular variance, and multilocus coalescent analyses. Results Significant inter‐population variation in allelic and haplotypic frequencies were observed (nuclear DNA F_ST = 0.004–0.290; mtDNA Φ_ST = 0.051–0.927). Whereas spatial differentiation in nuclear genes was concordant with subspecific designations, geographic proximity was more predictive of inter‐population variance in mitochondrial DNA haplotype frequency. Inferences of historical population demography were consistent with restriction of common eiders to four geographic areas during the Last Glacial Maximum: Belcher Islands, Newfoundland Bank, northern Alaska and Svalbard. Three of these areas coincide with previously identified glacial refugia: Newfoundland Bank, Beringia and Spitsbergen Bank. Gene‐flow and clustering analyses indicated that the Beringian refugium contributed little to common eider post‐glacial colonization of North America, whereas Canadian, Scandinavian and southern Alaskan post‐glacial colonization is likely to have occurred in a stepwise fashion from the same glacial refugium. Main conclusions Concordance of proposed glacial refugia used by common eiders and other Arctic species indicates that Arctic and subarctic refugia were important reservoirs of genetic diversity during the Pleistocene. Furthermore, suture zones identified at MacKenzie River, western Alaska/Aleutians and Scandinavia coincide with those identified for other Arctic vertebrates, suggesting that these regions were strong geographic barriers limiting dispersal from Pleistocene refugia.     

Searching for and Revealing Pleistocene Refugia of <Emphasis Type="Italic">Pinus sylvestris</Emphasis> L. in Central Yakutia

As a result of allozyme analysis, Nei’s genetic distances were determined between the phylogeographic group of seven populations of Pinus sylvestris L. in the “glacial” zone of the range in Central Yakutia and 25 populations of its hypothetical Pleistocene refugia of the southern nonglacial zone within the entire range of the species in Northern Eurasia. The location of the most likely “avant-garde” refugium of the modern yakutian populations of the Scots pine is Northern Priamur’e (Tynda), as well as less likely Siberian (Romanovka, Irkutsk), South Ural (Kryktytau), and Central European (the Czech Republic) refugia.     

Chloroplast DNA phylogeography of a distylous shrub (Palicourea padifolia, Rubiaceae) reveals past fragmentation and demographic expansion in Mexican cloud forests

Several phylogeographic studies in northern Mesoamerica have examined the influence of Pleistocene glaciations on the genetic structure of temperate tree species with their southern limit by the contact zone between species otherwise characteristic of North or South America, but few have featured plant species that presumably colonized northern Mesoamerica from South America. A phylogeographical study of Palicourea padifolia, a fleshy-fruited, bird dispersed distylous shrub, was conducted to investigate genetic variation at two chloroplast regions (trnS-trnG and rpl32-trnL) across cloud forest areas to determine if such patterns are consistent with the presence of Pleistocene refugia and/or with the historical fragmentation of the Mexican cloud forests. We conducted population and spatial genetic analyses as well as phylogenetic and isolation with migration analyses on 122 individuals from 22 populations comprising the distribution of P. padifolia in Mexico to gain insight of the evolutionary history of these populations. Twenty-six haplotypes were identified after sequencing 1389 bp of chloroplast DNA. These haplotypes showed phylogeographic structure (N(ST) = 0.508, G(ST) = 0.337, N(ST) > G(ST), P < 0.05), including a phylogeographic break at the Isthmus of Tehuantepec, with private haplotypes at either side of the isthmus, and a divergence time of the split in the absence of gene flow dating back c. 309,000-103,000 years ago. The patterns of geographic structure found in this study are consistent with past fragmentation and demographic range expansion, supporting the role of the Isthmus of Tehuantepec as a biogeographical barrier in the dispersal of P. padifolia. Our data suggest that P. padifolia populations were isolated throughout glacial cycles by the Isthmus of Tehuantepec, accumulating genetic differences due to the lack of migration across the isthmus in either direction, but the results of our study are not consistent with the existence of the previously proposed Pleistocene refugia for rain forest plant species in the region.