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.     

DECOUPLING OF SHORT‐ AND LONG‐DISTANCE DISPERSAL PATHWAYS IN THE ENDEMIC NEW ZEALAND SEAWEED CARPOPHYLLUM MASCHALOCARPUM (PHAEOPHYCEAE,FUCALES)1

The processes that produce and maintain genetic structure in organisms operate at different timescales and on different life‐history stages. In marine macroalgae, gene flow occurs through gamete/zygote dispersal and rafting by adult thalli. Population genetic patterns arise from this contemporary gene flow interacting with historical processes. We analyzed spatial patterns of mitochondrial DNA variation to investigate contemporary and historical dispersal patterns in the New Zealand endemic fucalean brown alga Carpophyllum maschalocarpum (Turner) Grev. Populations bounded by habitat discontinuities were often strongly differentiated from adjoining populations over scales of tens of kilometers and intrapopulation diversity was generally low, except for one region of northeast New Zealand (the Bay of Plenty). There was evidence of strong connectivity between the northern and eastern regions of New Zealand’s North Island and between the North and South Islands of New Zealand and the Chatham Islands (separated by 650 km of open ocean). Moderate haplotypic diversity was found in Chatham Islands populations, while other southern populations showed low diversity consistent with Last Glacial Maximum (LGM) retreat and subsequent recolonization. We suggest that ocean current patterns and prevailing westerly winds facilitate long‐distance dispersal by floating adult thalli, decoupling genetic differentiation of Chatham Island populations from dispersal potential at the gamete/zygote stage. This study highlights the importance of encompassing the entire range of a species when inferring dispersal patterns from genetic differentiation, as realized dispersal distances can be contingent on local or regional oceanographic and historical processes.     

Closing the gap: Avian lineage splits at a young,narrow seaway imply a protracted history of mixed population response

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β‐fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide‐ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island—South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.     

Comparative physiological studies on the growth of cryptic species of Bostrychia intricata (Rhodomelaceae,Rhodophyta) in various salinity and temperature conditions

Inter‐ and intra‐specific physiological variations of intertidal macroalgae have been well investigated. However, studies on physiological responses of cryptic algal species have been poorly documented. Bostrychia intricata is a widespread marine red alga in the Southern Hemisphere, and has many cryptic species. We investigated the effect of different salinities and temperatures on the specific growth rate of three cryptic species (N2, N4 and N5) of B. intricata from New Zealand. Our data indicated that all cryptic species grew at the full range of salinities and temperatures tested, but exhibited a significant difference in their specific growth rates. Cryptic species N4 had a higher growth rate than the other two cryptic species under all experimental conditions, whereas cryptic species N2 occasionally showed a higher growth rate than cryptic species N5 at high salinities and lower temperatures. The distinct physiological properties of these cryptic species may explain their distribution pattern (a wider distribution of cryptic species N4 than N2 and N5) in New Zealand. The physiological divergence between the cryptic species could be related to their levels of evolutionary divergence, with more similar physiology between cryptic species, which share a more recent common ancestor (N2 and N5). Our findings underline that morphologically indistinguishable cryptic algal species are different in many other aspects and are truly independent entities.     

High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction

The maintenance of genetic diversity is thought to be fundamental for the conservation of threatened species. It is therefore important to understand how genetic diversity is affected by the re-introduction of threatened species. We use establishment history and genetic data from the remnant and re-introduced populations of a New Zealand endemic bird, the hihi Notiomystis cincta, to understand genetic diversity loss and quantify the genetic effects of re-introduction. Our data do not support any recent bottleneck events in the remnant population. Furthermore, all genetic diversity measures indicate the remnant hihi population has retained high levels of genetic diversity relative to other New Zealand avifauna with similar histories of decline. Genetic diversity (N(A) , alleles per locus, allelic richness, F(IS) and H(S) ) did not significantly decrease in new hihi populations founded through re-introduction when compared to their source populations, except in the Kapiti Island population (allelic richness and H(S) ) which had very slow post-re-introduction population growth. The N(e) /N(c) ratio in the remnant population was high, but decreased in first-level re-introductions, which together with significant genetic differentiation between populations (F(ST) & Fisher's exact tests) suggest that extant populations are diverging as a result of founder effects and drift. Importantly, simulations of future allele loss predict that the number of alleles lost will be higher in populations with a slow population growth, fewer founding individuals and with nonrandom mating. Interestingly, this species has very high levels of extra-pair paternity which may reduce reproductive variance by allowing social and floater males to reproduce a life history trait that together with a large remnant population size may help maintain higher levels of genetic diversity than expected.     

Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China

Climate oscillations are the key factors to understand the patterns in modern biodiversity. East Asia harbors the most diverse temperate flora, largely because an extensive terrestrial ice cap was absent during repeated Pleistocene glaciation–interglacial cycles. Comparing the demographic histories of species that are codistributed and are close relatives may provide insight into how the process of climate change influences species ranges. In this study, we compared the spatial genetic structure and demographic histories of two coexisting Eleutherococcus species, Eleutherococcus senticosus and E. sessiliflorus. Both species are distributed in northern China, regions that are generally considered to be sensitive to climatic fluctuations. These regions once hosted temperate forest, but this temperate forest was replaced by tundra and taiga forest during the Last Glacial Maximum (LGM), according to pollen records. Using three chloroplast DNA fragments, we assessed the genetic structure of 20 and 9 natural populations of E. senticosus and E. sessiliflorus, respectively. Extremely contrasting genetic patterns were found between the two species; E. sessiliflorus had little genetic variation, whereas E. senticosus had considerably higher levels of genetic variation (15 haplotypes). We speculated that a recent severe bottleneck may have resulted in the extremely low genetic diversity in E. sessiliflorus. In E. senticosus, populations in Northeast China (NEC) harbored all of the haplotypes found in this species and included private haplotypes. The populations in NEC had higher levels of genetic diversity than did those from North China (NC). Therefore, we suggest that both the NC and NEC regions can sustain LGM refugia and that lineage admixture from multiple refugia took place after the LGM elevated the local genetic diversity in NEC. In NEC, multiple genetic hot spots were found in the Changbai Mountains and the Xiaoxing'an Range, which implied that multiple locations in NEC may sustain LGM refugia, even in the Xiaoxing'an Range.     

Comparative phylogeography of two Agarophyton species in the New Zealand archipelago

Molecular studies have reported the coexistence of two species of Agarophyton in New Zealand: the newly described A.transtasmanicum with an apparently restricted distribution to some sites in the North Island, and the more widespread A.chilense. Here, we compared the distribution, genetic diversity, and structure of both Agarophyton species throughout the archipelago using sequences of the nuclear Internal Transcribed Spacer 2 (ITS2) marker. Agarophyton chilense’s distribution was continuous and extensive along the North and South Islands, Stewart Island, and Chatham Island, and the genetic clusters were mostly concordant with boundaries between biogeographic regions. In contrast, specimens of A.transtasmanicum were collected in four sites broadly distributed in both the North and South Islands, with no clear spatial structure of the genetic diversity. Populations, where the species co-occurred, tended to display similar levels in genetic diversity for the two species. Demographic inferences supported a postglacial demographic expansion for two A.chilense genetic clusters, one present in the South Island and the eastern coast of the North Island, and the other present in northern South Island. A third genetic cluster located on the western coast of the North Island had a signature of long-term demographic stability. For A.transtasmanicum, the skyline plot also suggested a postglacial demographic expansion. Last, we developed a new molecular tool to quickly and easily distinguish between the two Agarophyton species, which could be used to ease future fine-scale population studies, especially in areas where the two species coexist.     

Population genetic connectivity of an endemic New Zealand passerine after large‐scale local extirpations: a model of re‐colonization potential

Little is known about how a 70% loss of native forests has affected the genetic connectivity of remnant bird populations in New Zealand. We use the common and widely distributed New Zealand Bellbird Anthornis melanura as an indicator species of population connectivity for well‐flighted birds. Using eight microsatellite loci, we identified five main genetic populations in the North Island, South Island, sub‐Antarctic Auckland Islands and two small remnant island populations adjacent to a large region of avian extirpations in northern North Island. Only one remnant island population, on a 30‐year‐old conservation reserve at Tiritiri Matangi, displayed a clear signature of recent genetic bottleneck. The 7% migration rate at Tiritiri Matangi indicates that bottlenecks can be maintained despite habitat rehabilitation, possibly through behavioural barriers to gene flow. Adjacent to the same extirpation zone, Bellbirds on the Poor Knights Islands were found to have low genetic diversity and low re‐colonization potential. Two gaps concordant with deforestation patterns separated the Kapiti Coast of southern North Island from populations to both the north and the south. In summary, we identified linked avian habitats, as well as isolated and inbred populations and suggest that Bellbirds are good re‐colonizers. We emphasize the importance of genetic studies that assess animal dispersal among newly rehabilitated habitat patches.     

One haploid parent contributes 100% of the gene pool for a widespread species in northwest North America

The monoicous peatmoss Sphagnum subnitens has a tripartite distribution that includes disjunct population systems in Europe (including the Azores), northwestern North America and New Zealand. Regional genetic diversity was highest in European S. subnitens but in northwestern North America, a single microsatellite‐based multilocus haploid genotype was detected across 16 sites ranging from Coos County, Oregon, to Kavalga Island in the Western Aleutians (a distance of some 4115 km). Two multilocus haploid genotypes were detected across 14 sites on South Island, New Zealand. The microsatellite‐based regional genetic diversity detected in New Zealand and North American S. subnitens is the lowest reported for any Sphagnum. The low genetic diversity detected in both of these regions most likely resulted from a founder event associated with vegetative propagation and complete selfing, with one founding haploid plant in northwest North America and two in New Zealand. Thus, one plant appears to have contributed 100% of the gene pool for the population systems of S. subnitens occurring in northwest North America, and this is arguably the most genetically uniform group of plants having a widespread distribution yet detected. Although having a distribution spanning 12.5° of latitude and 56° of longitude, there was no evidence of any genetic diversification in S. subnitens in northwest North America. No genetic structure was detected among the three regions, and it appears that European plants of S. subnitens provided the source for New Zealand and northwest North American populations.     

Identifying glacial refugia in a geographic parthenogen using palaeoclimate modelling and phylogeography: the New Zealand stick insect Argosarchus horridus (White)

We have used phylogeographic analysis of mitochondrial DNA (COI and COII genes) and ecological niche modelling (ENM) to reconstruct the population history of Argosarchus horridus (White), a widespread species of New Zealand stick insect. These data were used to address outstanding questions on the role of glacial refugia in determining the distribution and genetic structure of New Zealand species. Phylogeographic analysis shows a general pattern of high diversity in upper North Island and reduced diversity in lower North Island and South Island. The ENM indicates that during the last glacial maximum, A. horridus was largely restricted to refugia around coastal areas of North Island. The ENM also suggests refugia on the northeast coast of South Island and southeast coast of North Island and this prediction is verified by phylogeographic analysis, which shows a clade restricted to this region. Argosarchus horridus is also most likely a geographic parthenogen where males are much rarer at higher latitudes. The higher levels of genetic variation in northern, bisexual populations suggest southern and largely unisexual populations originated from southwardly expanding parthenogenetic lineages. Bayesian skyline analysis also provides support for a recent population size increase consistent with a large increase in geographic distribution in the late Pleistocene. These results exemplify the utility of integrating ENM and phylogeographic analysis in testing hypotheses on the origin of geographic parthenogenesis and effects of Pleistocene environmental change on biodiversity.     

High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae)

The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans‐Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified, and 29 of these haplotypes were restricted to single populations. The within‐population genetic diversity was high (mean h_S = 0.72), and among‐population genetic differentiation showed a strong phylogeographic structure (N_ST = 0.630 > G_ST = 0.266; p < .001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure, and ecological niche models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.     

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.     

Phylogeographic-based conservation implications for the New Zealand long-tailed bat, (<Emphasis Type="Italic">Chalinolobus tuberculatus</Emphasis>): identification of a single ESU and a candidate population for genetic rescue

The New Zealand long-tailed bat (Chalinolobus tuberculatus) is an endemic species threatened with extinction. Since the arrival of humans, massive deforestation has occurred and invasive mammalian predators were introduced. As a result, C. tuberculatus’ distribution shrank dramatically and became fragmented. To aid the management of the remaining populations, two Evolutionary Significant Units (ESUs) were designated: one on each of New Zealand’s main islands. We utilised mitochondrial sequence data (cytb, 703 bp) and 10 nuclear DNA microsatellite loci to reconstruct the demographic history of this species, to characterise the level of genetic diversity in remaining populations, and to assess the current connectivity between them. Our results indicate that the North Island, with the highest genetic diversity, served as a glacial refuge, with a loss of diversity following the path recolonization to the south of the South Island. However, our data are also consistent with continued, or at least very recent, genetic exchange between colonies across the species distribution. The only exception is the Hanging Rock colony on the east coast of the South Island, which appears to be isolated. Thus, there was no support for the previously designated ESUs. Signatures of past population declines were found in three colonies, the most extreme of which was found in Hanging Rock. Consequently, we recommend that it be genetically rescued via translocation from a donor population. In general, future management priorities should treat Chalinolobus tuberculatus as a single unit, focusing on maintaining connectivity between remaining populations, together with continued roost protection and pest control.     

Life‐history predicts past and present population connectivity in two sympatric sea stars

Life‐history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution but have been equivocal in this regard. Here, we sample two sympatric sea stars across the same geographic range in temperate waters of Australia. Using a combination of mitochondrial DNA sequences, nuclear DNA sequences, and microsatellite genotypes, we show that the benthic‐developing sea star, Parvulastra exigua, has lower levels of within‐ and among‐population genetic diversity, more inferred genetic clusters, and higher levels of hierarchical and pairwise population structure than Meridiastra calcar, a species with planktonic development. While both species have populations that have diverged since the middle of the second glacial period of the Pleistocene, most P. exigua populations have origins after the last glacial maxima (LGM), whereas most M. calcar populations diverged long before the LGM. Our results indicate that phylogenetic patterns of these two species are consistent with predicted dispersal abilities; the benthic‐developing P. exigua shows a pattern of extirpation during the LGM with subsequent recolonization, whereas the planktonic‐developing M. calcar shows a pattern of persistence and isolation during the LGM with subsequent post‐Pleistocene introgression.     

Genetic diversity and historical population structure in the New Zealand mayfly Acanthophlebia cruentata

1. Nucleotide sequences of a 280 base pair region of the cytochrome b gene were used to assess genetic diversity and to infer population histories in the New Zealand mayfly Acanthophlebia cruentata. 2. A hierarchial examination of populations from 19 streams at different spatial scales in the central and northern North Island of New Zealand found 34 haplotypes. A common haplotype was found in all central region streams and unique haplotypes in northern streams. Several central streams had region specific haplotypes with genetically differentiated populations at the 70–100 km scale. 3. Haplotype diversity was high (0.53–0.8) at most sites, but low (0–0.22) in some central sites. amova analyses found significant genetic diversity among regions (69%) and among catchments (58%). Most population pairwise F_ST tests were significant, with non‐significant pairwise tests among sites in the central region and pairs of sites between neighbouring streams. 4. The levels of sequence divergence are interpreted as the result of Pleistocene divergence in multiple refugia, leading to the evolution of regionally unique haplotypes. The low diversity in some central region populations may result from recent colonisation following local extinctions, associated with volcanic events.     

Population structure and biogeography of Hemiphaga pigeons (Aves: Columbidae) on islands in the New Zealand region

Aim The New Zealand avifauna includes lineages that lack close relatives elsewhere and have low diversity, characteristics sometimes ascribed to long geographic isolation. However, extinction at the population and species levels could yield the same pattern. A prominent example is the ecologically important pigeon genus Hemiphaga. In this study, we examined the population structure and phylogeography of Hemiphaga across islands in the region. Location New Zealand, Chatham Islands and Norfolk Island. Methods Mitochondrial DNA was sequenced for all species of the genus Hemiphaga. Sixty‐seven individuals from mainland New Zealand (Hemiphaga novaeseelandiae novaeseelandiae), six of the Chatham Islands sister species (Hemiphaga chathamensis), and three of the extinct Norfolk Island subspecies (Hemiphaga novaeseelandiae spadicea) were included in this study. Novel D‐loop and cytochrome b primers were designed to amplify DNA from museum samples. Additionally, five other mitochondrial genes were used to examine placement of the phylogenetic root. Results Analyses of mitochondrial DNA sequences revealed three Hemiphaga clades, consistent with the allopatric populations of recognized (sub)species on oceanic islands. Of the 23 D‐loop haplotypes among 67 New Zealand pigeons (Hemiphaga n. novaeseelandiae), 19 haplotypes were singletons and one haplotype was common and widespread. Population genetic diversity was shallow within and between New Zealand populations, indicating range expansion with high inter‐population exchange. Tentative rooting of the Hemiphaga clade with cyt b data indicates exchange between mainland New Zealand and the Chatham Islands prior to colonization of Norfolk Island. We found low genetic divergence between populations on New Zealand, the Chatham Islands and Norfolk Island, but deep phylogenetic divergence from the closest living relatives of Hemiphaga. Main conclusions The data are consistent with the hypothesis of population reduction during the Pleistocene and subsequent expansion from forest refugia. Observed mobility of Hemiphaga when feeding helps explain the shallow diversity among populations on islands separated by many hundreds of kilometres of ocean. Together with comparison of distribution patterns observed among birds of the New Zealand region, these data suggest that endemicity might represent not long occupancy of an area, but descent from geologically recent colonizations. We consider the role of lineage pruning in creating the impression of old endemicity.     

Characterization of MHC class II B polymorphism in bottlenecked New Zealand saddlebacks reveals low levels of genetic diversity

The major histocompatibility complex (MHC) is integral to the vertebrate adaptive immune system. Characterizing diversity at functional MHC genes is invaluable for elucidating patterns of adaptive variation in wild populations, and is particularly interesting in species of conservation concern, which may suffer from reduced genetic diversity and compromised disease resilience. Here, we use next generation sequencing to investigate MHC class II B (MHCIIB) diversity in two sister taxa of New Zealand birds: South Island saddleback (SIS), Philesturnus carunculatus, and North Island saddleback (NIS), Philesturnus rufusater. These two species represent a passerine family outside the more extensively studied Passerida infraorder, and both have experienced historic bottlenecks. We examined exon 2 sequence data from populations that represent the majority of genetic diversity remaining in each species. A high level of locus co-amplification was detected, with from 1 to 4 and 3 to 12 putative alleles per individual for South and North Island birds, respectively. We found strong evidence for historic balancing selection in peptide-binding regions of putative alleles, and we identified a cluster combining non-classical loci and pseudogene sequences from both species, although no sequences were shared between the species. Fewer total alleles and fewer alleles per bird in SIS may be a consequence of their more severe bottleneck history; however, overall nucleotide diversity was similar between the species. Our characterization of MHCIIB diversity in two closely related species of New Zealand saddlebacks provides an important step in understanding the mechanisms shaping MHC diversity in wild, bottlenecked populations.     

Quaternary climate instability is correlated with patterns of population genetic variability in Bombus huntii

Climate oscillations have left a significant impact on the patterns of genetic diversity observed in numerous taxa. In this study, we examine the effect of Quaternary climate instability on population genetic variability of a bumble bee pollinator species, Bombus huntii in western North America. Pleistocene and contemporary B. huntii habitat suitability (HS) was estimated with an environmental niche model (ENM) by associating 1,035 locality records with 10 bioclimatic variables. To estimate genetic variability, we genotyped 380 individuals from 33 localities at 13 microsatellite loci. Bayesian inference was used to examine population structure with and without a priori specification of geographic locality. We compared isolation by distance (IBD) and isolation by resistance (IBR) models to examine population differentiation within and among the Bayesian inferred genetic clusters. Furthermore, we tested for the effect of environmental niche stability (ENS) on population genetic diversity with linear regression. As predicted, high‐latitude B. huntii habitats exhibit low ENS when compared to low‐latitude habitats. Two major genetic clusters of B. huntii inhabit western North America: (a) a north genetic cluster predominantly distributed north of 28°N and (b) a south genetic cluster distributed south of 28°N. In the south genetic cluser, both IBD and IBR models are significant. However, in the north genetic cluster, IBD is significant but not IBR. Furthermore, the IBR models suggest that low‐latitude montane populations are surrounded by habitat with low HS, possibly limiting dispersal, and ultimately gene flow between populations. Finally, we detected high genetic diversity across populations in regions that have been climatically unstable since the last glacial maximum (LGM), and low genetic diversity across populations in regions that have been climatically stable since the LGM. Understanding how species have responded to climate change has the potential to inform management and conservation decisions of both ecological and economic concerns.     

The population demography of Betula maximowicziana,a cool‐temperate tree species in Japan,in relation to the last glacial period: its admixture‐like genetic structure is the result of simple population splitting not admixing

Conservation of the local genetic variation and evolutionary integrity of economically and ecologically important trees is a key aspect of studies involving forest genetics, and a population demographic history of the target species provides valuable information for this purpose. Here, the genetic structure of 48 populations of Betula maximowicziana was assessed using 12 expressed sequence tag–simple sequence repeat (EST‐SSR) markers. Genetic diversity was lower in northern populations than southern ones and structure analysis revealed three groups: northern and southern clusters and an admixed group. Eleven more genomic‐SSR loci were added and the demographic history of these three groups was inferred by approximate Bayesian computation (ABC). The ABC revealed that a simple split scenario was much more likely than isolation with admixture, suggesting that the admixture‐like structure detected in this species was due to ancestral polymorphisms. The ABC analysis suggested that the population growth and divergence of the three groups occurred 96 800 (95% CI, 20 500–599 000) and 28 300 (95% CI, 8700–98 400) years ago, respectively. We need to be aware of several sources of uncertainty in the inference such as assumptions about the generation time, overlapping of generations, confidence intervals of the estimated parameters and the assumed model in the ABC. However, the results of the ABC together with the model‐based maps of reconstructed past species distribution and palaeoecological data suggested that the modern genetic structure of B. maximowicziana originated prior to the last glacial maximum (LGM) and that some populations survived in the northern range even during the LGM.     

Deeply divergent lineages of the widespread New Zealand amphipod Paracalliope fluviatilis revealed using allozyme and mitochondrial DNA analyses

1. We evaluated the population genetic structure of the common New Zealand amphipod Paracalliope fluviatilis using eight allozyme loci, and the mitochondrial cytochrome oxidase c subunit I (COI) gene locus. Morphological analyses were also conducted to evaluate any phenotypic differences. Individuals belonging to P. fluviatilis were collected from a total of 14 freshwater fluvial habitats on the North and South Islands, New Zealand. 2. We found evidence for strong genetic differentiation among locations (Wright's F_ST > 0.25), and fixed differences (non‐shared alleles) at two of the eight allozyme loci indicating the possibility of previously unknown species. Analysis of a 545‐bp fragment of the COI locus was mostly congruent with the allozyme data and revealed the same deeply divergent lineages (sequence divergences up to 26%). 3. Clear genetic breaks were identified between North Island and South Island populations. North Island populations separated by <100 km also showed genetic differences between east and west draining watersheds (sequence divergence >12%). Accordingly, present‐day dispersal among hydrologically isolated habitats appears minimal for this taxon. 4. Although population differences were clearly shown by allozyme and mtDNA analyses, individuals were morphologically indistinguishable. This suggests that, as in North American and European taxa (e.g. Hyalella and Gammarus), morphological conservatism may be prevalent among New Zealand's freshwater amphipods. We conclude that molecular techniques, particularly the COI gene locus, may be powerful tools for resolving species that show no distinctive morphological differences.