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New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades.

Density-dependent processes play a key role in the spatial structuring of biodiversity. Specifically, interrelated demographic processes, such as gene surfing, high-density blocking, and competitive exclusion, can generate striking geographic contrasts in the distributions of genes and species. Here, we propose that well-studied evolutionary and ecological biogeographic patterns of postglacial recolonization, progressive island colonization, microbial sectoring, and even the 'Out of Africa' pattern of human expansion, are fundamentally similar, underpinned by a 'founder takes all' density-dependent principle. Additionally, we hypothesize that older historic constraints of density-dependent processes are seen today in the dramatic biogeographic shifts that occur in response to human-mediated extinction events, whereby surviving lineages rapidly expand their ranges to replace extinct sister taxa., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Phylogeographic and evolutionary research programmes have successfully elucidated compelling genetic signatures of earth history. Particularly influential achievements include the demonstration of postglacial recolonization patterns for high-latitude taxa and phylogenetic demonstration of the 'progression rule' along oceanic island chains such as Hawaii. While both of these major biogeographic patterns clearly rely on rapid dispersal over long distances, their phylogeographic detection also apparently relies on the competitive exclusion of secondary dispersers. Such exclusion could occur either between or within species and might reflect fitness differences between lineages or, alternatively, neutral demographic processes (e.g. 'high-density blocking'). Regardless, such spatial genetic patterns would be rapidly eroded were it not for the failure of subsequent dispersers to contribute genetically to newly colonized populations. In addition to its role in revealing colonization patterns, competitive exclusion may also explain the maintenance of historic phylogeographic disjunctions long after the original physical barriers to dispersal have ceased to exist. Additionally, some of the most persuasive evidence of competitive exclusion comes from studies of anthropogenic extinction, where surviving lineages have subsequently expanded their ranges, apparently benefitting from the demise of their prehistoric sisters. Broadly, these biogeographic paradigms are united by the 'disconnect' between dispersal and colonization success, the latter being heavily influenced by inter- and intraspecific competition. Despite its apparent importance, such exclusion (especially within species) has received virtually no attention in the phylogeographic literature. Future studies should aim to test directly for the role of competitive exclusion in constraining the biogeography of highly dispersive taxa., (© 2011 Blackwell Publishing Ltd.)

Coastal populations are often connected by unidirectional current systems, but the biological effects of such asymmetric oceanographic connectivity remain relatively unstudied. We used mtDNA analysis to determine the phylogeographic origins of beach-cast bull-kelp (Durvillaea antarctica) adults in the Canterbury Bight, a 180 km coastal region devoid of rocky-reef habitat in southern New Zealand. A multi-year, quantitative analysis supports the oceanographically derived hypothesis of asymmetric dispersal mediated by the north-flowing Southland Current. Specifically, 92% of beach-cast specimens examined had originated south of the Bight, many drifting north for hundreds of kilometres, and some traversing at least 500 km of ocean from subantarctic sources. In contrast, only 8% of specimens had dispersed south against the prevailing current, and these counter-current dispersers likely travelled relatively small distances (tens of kilometres). These data show that oceanographic connectivity models can provide robust estimates of passive biological dispersal, even for highly buoyant taxa. The results also indicate that there are no oceanographic barriers to kelp dispersal across the Canterbury Bight, indicating that other ecological factors explain the phylogeographic disjunction across this kelp-free zone. The large number of long-distance dispersal events detected suggests drifting macroalgae have potential to facilitate ongoing connectivity between otherwise isolated benthic populations., (© 2010 Blackwell Publishing Ltd.)

Long-distance dispersal (LDD) is thought to be a key driver of biogeographic processes, yet few direct natural observations have been made of this process. Several studies have characterised diverse benthic epibiotic communities associated with buoyant macroalgae and have proposed that kelp rafting may be an important LDD mechanism for such coastal species. We test for LDD by combining biological, genetic, and geological data from rafted bull-kelp (Durvillaea antarctica) specimens collected in southern New Zealand following a March 2018 storm. Genetic and ecological data strongly indicate that three of 29 detached kelp specimens sequenced (and their associated live epifaunal taxa) had rafted from the sub-Antarctic to mainland New Zealand, traversing both oceanographic and phylogeographic barriers, over the course of an approximately 4-week journey. Numerous additional epifaunal taxa were detected from rafts that had geologically-distant mainland origins. The successful trans-oceanic rafting documented for sub-Antarctic brooding sea-star, chiton and sea-slug taxa presents a mechanism for their broad but phylogeographically disjunct Southern Hemisphere distributions. Moreover, the detection of several such LDD events over the last decade suggests that such journeys are very common over evolutionary timeframes. Although geological and genetic data were informative over different scales, we detected no conflict between the inferences from these distinct data sets, a finding that reinforces the value of integrative approaches to marine biogeography.

Large‐scale disturbance events provide ideal opportunities to directly study recolonisation processes in natural environments, via the removal of competitors and the formation of newly vacant habitat. A high magnitude earthquake in central New Zealand in 2016 created major ecological disturbance, with coastal tectonic uplift of up to ~ 6 m extirpating vast swathes of intertidal organisms. One of the affected species was Durvillaea antarctica (rimurapa or southern bull kelp), which is an important habitat‐forming intertidal macroalga capable of long‐distance dispersal. Across the complex fault system with varying amounts of uplift, the species was either locally extirpated or heavily reduced in abundance. We hypothesised that neutral priority effects and chance dispersal from other populations would influence which lineages would establish. We sampled individuals of D. antarctica across the uplift zone immediately after the earthquake in 2016 and then repeatedly sampled new recruits in the same areas between 2017 and 2020, using genotyping‐by‐sequencing to provide 'before' and 'after' genomic comparisons. Our results revealed strong geographic clustering but little evidence of new lineages establishing at disturbed sites, although populations at uplifted sites remain at remarkably low densities. We infer that recolonisation has thus far primarily originated from refugial, remnant patches within the uplift zone. To complement the phylogeographic analysis, we estimated oceanographic connectivity among the uplift zone sample locations. The connectivity modelling estimated that northbound dispersal of D. antarctica was more likely, but we have not yet detected southern genotypes in the recolonised populations. As the ongoing recolonisation process transitions from an ecological to an evolutionary timescale, change remains possible. This study provides the first genomic 'snapshots' of a natural recolonisation process following a large‐scale ecological disturbance event, and ongoing research has the potential to reveal important insight into both micro‐ and macroevolutionary processes. [ABSTRACT FROM AUTHOR]

Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time‐calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts. [ABSTRACT FROM AUTHOR]

Aim: Genotyping‐by‐sequencing (GBS) and similar reduced‐representation sequencing methods, such as restriction site‐associated DNA sequencing (RADseq), have been revolutionary for genetic analyses in biogeography. However, navigating the many different methodological and analytical approaches and numerous sources of potential error can be overwhelming. We provide an overview of key considerations for biogeographical research using GBS, from sample design through data filtering to the sharing of data, which should particularly assist new users. Taxon: All taxa. Location: Worldwide. Methods: We review recent advances for GBS and compare differences among GBS methods and analytical approaches. We highlight the concerns most relevant for biogeographical research, and emphasise practical limitations for studies on non‐model organisms. Results: GBS methods vary substantially and recent literature demonstrates the need for careful study design and data filtering relevant to the study organism and hypothesis under investigation. Biogeographical research using non‐model organisms or long‐term sampling are likely to face some practical limitations compared to ideal GBS study designs. The methodological information recorded in published manuscripts often varies. We outline a general framework for planning and undertaking biogeographical research using GBS. Main conclusions GBS and similar approaches have grown rapidly in popularity for biogeographical research. Evaluating, recording and justifying decisions throughout a GBS workflow—across sampling, library preparation and sequencing, identifying and filtering samples and loci, biogeographical analyses, and sharing data—is crucial for improving scientific reproducibility and compatibility among GBS datasets. This review outlines ways to improve and simplify GBS research, thereby enhancing our capacity to use genomic data to address broad‐scale biogeographical questions. [ABSTRACT FROM AUTHOR]

Aim: Coastal habitats are among the most dynamic environments on earth and are highly vulnerable to large‐scale physical disturbance. Genetic studies of nearshore marine species are revealing long‐lasting signatures of major coastal disturbance events. We synthesize emerging data to highlight how physical perturbations can impact the phylogeographic patterns of coastal populations. Taxon: Coastal marine and estuarine taxa. Location: Coastal regions around the globe. Methods: We synthesize coastal genetic and genomic literature, focussing particularly on the phylogeographic consequences of natural disturbance events including uplift, tsunami, hurricanes, glaciations and sea‐level fluctuations. We focus on studies with clear physical analytical frameworks constrained by abiotic data. Results: Tectonic and atmospheric disruptions can be considered shot‐term events with major impacts on populations adjacent to the centre of disturbance, typically resulting in the evolution of shallow phylogeographic patterns. Long‐lived climate‐driven disturbances such as glaciations, however, operate over vast geographic scales and often drive deep evolutionary patterns in affected populations. We show that studies using genome‐wide data could better identify fine‐scale signatures of both past and contemporary habitat perturbations. Conclusions: Recent data reveal the interplay between physical upheaval and coastal phylogeography, indicating that disturbance can affect diversity, connectivity and demography of coastal populations. The interplay between long‐lived large‐scale disturbance and species‐specific biotic traits has shaped deep phylogeographic patterns of coastal taxa. Additionally, it could be argued that, at least for some regions, short‐term disturbance is the 'rule' rather than the 'exception', and thus, represents a key driver of coastal genetic patterns in disturbance prone coastal regions. Geo‐genomic approaches that combine genome‐wide data with explicit habitat models or disturbance history information have been particularly successful in explaining the drivers of coastal evolutionary change. We argue that future integration of genomic and physical data will be crucial for tracing evolutionary trends in fast‐changing marine environments. [ABSTRACT FROM AUTHOR]

Large‐scale disturbance events have the potential to drastically reshape biodiversity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonized by multiple lineages, which can lead to the evolution of distinct spatial "sectors" of genetic diversity within a species. We test for disturbance‐driven sectoring of genetic diversity in intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot, following the high‐magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping‐by‐sequencing (GBS) to analyse fine‐scale population structure across the uplift zone and apply machine learning to assess the fit of alternative recolonizaton models. Our analysis reveals that specimens from the uplift zone carry distinctive genomic signatures potentially linked to post‐earthquake recolonization processes. Specifically, our analysis identifies two parapatric spatial‐genomic sectors of D. antarctica at Turakirae Head, which experienced the most dramatic uplift. Based on phylogeographical modelling, we infer that bull kelp in the Wellington region was probably a source for recolonization of the heavily uplifted Turakirae Head coastline, via two parallel, eastward recolonization events. By identifying multiple parapatric genotypic sectors within a recently recolonized coastal region, the current study provides support for the hypothesis that competing lineage expansions can generate striking spatial structuring of genetic diversity, even in highly dispersive taxa. [ABSTRACT FROM AUTHOR]

Aim: Understanding how natural populations respond to climatic shifts is a fundamental goal of biological research in a fast‐changing world. The Southern Ocean represents a fascinating system for assessing large‐scale climate‐driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. Blue‐eyed shags represent a paradoxical seabird radiation—a circumpolar distribution implies strong dispersal capacity yet their species‐rich nature suggests local adaptation and isolation. Here we attempt to resolve this paradox in light of the history of repeated cycles of climate change in the Southern Ocean. Location: Southern Ocean. Taxa: 16 species and subspecies of blue‐eyed shags (Phalacrocoracidae; Leucocarbo spp.). Methods: We use mitochondrial and nuclear sequence data from individuals across the geographical range of the genus to conduct the first comprehensive, time‐calibrated phylogenetic analyses and ancestral‐range biogeographical reconstructions of the blue‐eyed shags. Results: The origins of many island‐endemic lineages are remarkably recent, consistent with a recent high‐latitude circumpolar radiation in the Pliocene or Early Pleistocene. This recent sub‐Antarctic expansion contrasts with significantly deeper lineages detected in South America and, to a lesser extent, New Zealand. These regions, particularly South America, acted as glacial refugia and sources for multiple waves of post‐glacial dispersal. Main conclusions: The blue‐eyed shag paradox is resolved, with at least two waves of dispersal, linked to interglacial cycles, explaining the current distribution and diversity. Descendants of a Pliocene or Early Pleistocene wave of dispersal out of South America survive in the New Zealand region. In contrast, taxa distributed on sub‐Antarctic islands originated much later, possibly since the Last Glacial Maximum. Blue‐eyed shags therefore represent a powerful model system—comprising several natural replicates—for studying the early stages of founder‐event speciation and adaptation in a Southern‐Ocean bird group. [ABSTRACT FROM AUTHOR]

Understanding the forces that shape species distributions is increasingly important in a fast‐changing world. Although major disturbance events can adversely affect natural populations, they can also present new opportunities, for example by opening up habitat for colonization by other lineages. Following extensive geographic sampling, we use genomic data to infer a range extension following disturbance for an ecologically important intertidal macroalgal species. Specifically, we genotyped 288 southern bull kelp (Durvillaea) plants from 28 localities across central New Zealand. All specimens from the North Island were expected to be D. antarctica, but unexpectedly 10 samples from four sites were identified as D. poha. Extensive sampling from the northern South Island (105 samples at five locations) confirmed the absence of D. poha north of the Kaikōura Peninsula. The North Island specimens of D. poha therefore reveal a biogeographic disjunction, some 150 km northeast of the nearest (South Island) population of this species. Based on strong geographic correspondence between these North Island samples and historic disturbance, we infer that tectonic upheaval, particularly earthquake‐generated landslides, likely extirpated local D. antarctica and created an opportunity for a northward range expansion event by D. poha. Close phylogenomic relationships between this new North Island population and South Island samples support a geologically recent northward expansion, rather than a deeper evolutionary origin. These findings indicate the potential of large‐scale disturbances to facilitate sudden biogeographic range expansions, and they emphasize the ability of genomic analyses with fine‐scale sampling to reveal long‐lasting signatures of past disturbance, dispersal, and colonization. [ABSTRACT FROM AUTHOR]

Island ecosystems can be severely affected by climate change as they provide limited opportunities for species to track their habitat. Studying the population dynamics of keystone species from these ecosystems can shed a light on climate – ecosystem interactions. Southern beeches are such keystone species in New Zealand with beech forests constituting the most abundant forest cover on the two main islands. Here we use 2.4 kilobase pairs of chloroplast genetic markers from four species of southern beech across their geographic distribution to help elucidate the Pleistocene history of New Zealand forests, and the processes that led to the present-day distribution of southern beech diversity. Broadly concordant phylogeographic patterns were observed across all beech species analysed. The centre of genetic diversity in silver beech was in the northern South Island, with unique haplotypes in the southern South Island, and southern and northern North Island, separated by known 'beech gaps'. Significantly less genetic diversity was evident in the subgenus Fuscospora (red, hard, black/mountain beech). All three species shared a single haplotype in the southern South Island, and a unique haplotype north of the central South Island 'beech gap'. Our study indicates that the present-day distribution of southern beech diversity in New Zealand is largely a result of Plio-Pleistocene environmental changes, with survival in cryptic southern South Island and multiple North Island in situ microrefugia throughout recent glacial cycles. By contrast, the northern South Island was likely the only New Zealand region that supported large (silver) beech populations throughout the Pleistocene. With beech species in New Zealand being keystone forest species, the distribution of the genus throughout the Pleistocene provides a proxy for forest cover at different times. It helps understand the ecological challenges the New Zealand forest fauna and flora were exposed to during the climate oscillations of the ice ages. [ABSTRACT FROM AUTHOR]

Aim: Repeated cycles of Pleistocene glaciation have influenced phylogeographic structure of taxa on New Zealand's South Island. Many taxa became restricted to refugia at either end of the island during glaciation, resulting in an area of low endemicity in central South Island. This area of low endemism is typified by the so‐called beech (or biotic) gap, where the absence of Nothofagus forest (and many other plant and invertebrate taxa) has been attributed to repeated glaciation. Some taxa, however, appear to have persisted in situ in localized refugia within the biotic gap. We test these alternative hypotheses in a large flightless alpine wētā (grasshopper). Location: Southern Alps, South Island, New Zealand. Taxon: Hemideina maori Pictet & Saussure, 1891 (Orthoptera: Anostostomatidae). Methods: We used phylogeographic analysis of mitochondrial cytochrome c oxidase I (cox1) and 25 nuclear DNA (nuDNA) markers to test for Pleistocene glacial microrefugia within the current montane South Island range of Hemideina maori. Results: We identified eight deeply differentiated mtDNA lineages with limited sharing of haplotypes among populations. Genetic differentiation assessed using nuDNA revealed a similar pattern, with three groups broadly corresponding to the deepest mtDNA splits. The central South Island region exhibits substantial endemic mtDNA diversity and a distinctive nuclear lineage. Main conclusions: These results indicate that H. maori likely persisted in microrefugia within the biotic gap during glaciation. These deep lineages are estimated to have started diverging prior to the initiation of glaciation, up to 3 Ma. These results add to a growing number of Southern Hemisphere examples of deep phylogeographic differentiation in glaciated alpine regions compared to Europe and North America, probably reflecting less intense glaciation. We suggest that other Southern Alps species showing northern and southern clades alone are more montane than alpine, and were reliant on warmer habitat to the north and south during glacial eras. Thus, there are species‐specific responses to climatic processes, influenced by distinctive habitat requirements and physiological traits. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Aim: Biological diversification can be substantially influenced by earth history. The links between biological and geological processes can be particularly tight for obligate freshwater biota. Here, we test for such links with respect to Pliocene shifts in drainage geometry of one of the Australia's largest river systems. Location: Major rivers of south‐eastern Australia. Taxon: Freshwater‐limited fishes and crayfish. Methods: We synthesize recently published geological and freshwater phylogeographic data to elucidate the evolutionary history of south‐eastern Australia's major river drainages and their biotas. Results: Recent data demonstrate how a major Pliocene drainage rearrangement event in the lower Murray‐Darling basin led to the evolution of a distinctive and "marooned" phylogeographic assemblage in the Glenelg and Wimmera drainages. Main conclusions: Biological data from southern Australia illuminate the region's geological history, and vice versa. Our study highlights the persisting evolutionary effects of a major Pliocene drainage rearrangement. The lasting geological and biological preservation of such an ancient tectonic event is apparently facilitated by Australia's uniquely stable geological setting. [ABSTRACT FROM AUTHOR]

Abstract: Recent studies have suggested that spatial patterns of intraspecific diversity can be influenced by density‐dependent processes, which can inhibit effective migration of new lineages to established populations. How mechanisms such as dispersal and disturbance influence these processes is, however, still poorly understood. We hypothesised that (1) species with leptokurtic dispersal (frequent on small scales but rare on larger scales) would show no spatial structure on small scales and strong structure on large scales, and (2) disturbance would influence the chance of genetic turnover in a population. We tested these hypotheses using empirical genetic (mtDNA) data from field observations of a model taxon (the buoyant, forest‐forming kelp Durvillaea, which exhibits leptokurtic dispersal distribution), and by conducting simulation analyses. Our data supported the first hypothesis, with no spatial structure detected on fine (metres) scales despite evidence of strong structure on larger (tens to hundreds of kilometres) scales. The second hypothesis was also supported, with simulations showing that disturbance increased the rate at which structure developed, and reduced the time to fixation (monopolisation by a single lineage). The chance of any lineage reaching fixation was directly related to its initial proportion in the population, and this relationship was unaffected by changes in disturbance size or dispersal capacity. We conclude that, in the absence of selection, extirpation is typically a prerequisite for population‐genetic “turnover”, with remnant (refugial) individuals otherwise outnumbering immigrants. Synthesis. Disturbance plays a critical role in releasing density‐dependent blocks to colonisation, and thus enables lineage turnover within species. Our results indicate that although both disturbance size and dispersal capacity play important roles in the formation of spatial structure within species, unless a population is totally extirpated, establishment of genetic lineages from elsewhere (turnover) is unlikely even for species that can disperse well. [ABSTRACT FROM AUTHOR]

Marine biogeographers have long speculated that macroalgal rafting presents a dispersal mechanism for brooding marine invertebrates of the Southern Ocean, but few direct observations of rafting by echinoderm taxa have been documented. Here we report rafting of the brooding benthic sea star Anasterias suteri, along with two mollusc taxa (Onithochiton neglectus - also a brooder - and Cantharidus roseus), on detached bull-kelp Durvillaea antarctica in Foveaux Strait, southern New Zealand. The rafting journey, intercepted at sea, likely lasted for 2-3 weeks and may have covered several hundred kilometres. We use DNA sequences, together with meteorological and prevailing oceanographic data, to infer the likely Fiordland (mainland) origins of the raft and its epifauna. This rafting dispersal mechanism provides an explanation for the broad (circum-subantarctic) but disjunct distribution of brooding Anasterias populations, and for the genetic connectivity observed between their populations. [ABSTRACT FROM AUTHOR]

The aeolid nudibranch Fiona pinnata (Eschscholtz, 1831) is an obligate rafter that occurs exclusively on macroalgal rafts and other floating substrata, and has a seemingly cosmopolitan marine distribution. Mitochondrial (mtDNA) and nuclear DNA sequence data were generated from specimens collected worldwide to test for global connectivity in this species. Phylogeographic analyses revealed three divergent mtDNA lineages, two of which were abundant and widespread. One of these lineages has an apparent circumequatorial distribution, whereas the other may have an antitropical distribution within the Pacific Ocean. Low genetic divergences within each lineage suggest that rafting can mediate dispersal across transoceanic scales. A third, highly divergent, lineage was detected in a single Indonesian specimen. Broadly concordant phylogeographic relationships were detected for the nuclear ITS1 region, with distinct tropical versus antitropical lineages observed. The substantial genetic divergences and largely allopatric distributions observed among the F. pinnata lineages suggest that they represent a species complex. [ABSTRACT FROM AUTHOR]

1. Understanding the ecological factors governing population connectivity in freshwater systems represents an ongoing challenge for aquatic biologists. 2. We used genetic analysis to test the hypothesis that fine-scale habitat preferences can influence within-river connectivity patterns in freshwater-limited fishes. 3. Genetic variation among sampling sites within systems was compared for co-distributed fish taxa Galaxias gollumoides (low-velocity pool/swamp habitat) versus an undescribed species, Galaxias 'southern' (high-velocity riffle habitat), using ø statistics. These analyses incorporated 1624 bp of mtDNA from 429 galaxiid specimens, encompassing 95 localities across four river systems in Southland, New Zealand. 4. Although similar numbers of haplotypes per river were detected in both taxa, spatial partitioning of this genetic variation within rivers was significantly stronger for G. gollumoides (mean øST 0.539) than for G. 'southern' (mean øST 0.142). Within-catchment genetic divergence values were also higher for the former species. 5. These finding suggest that a combination of main-channel habitat continuity and high water velocity facilitates relatively high connectivity in G. 'southern', whereas G. gollumoides populations are genetically isolated in fragmented low-velocity habitats. We conclude that population connectivity can be strongly influenced by habitat preference, leading to profound differences in the phylogeography, diversity and conservation status of freshwater fish lineages. [ABSTRACT FROM AUTHOR]

Aim To test the hypothesis that geomorphological features, shaped by underlying geology, can influence within-river connectivity patterns in freshwater-limited fishes. Location Rivers draining the eastern flanks of the Southern Alps in South Island, New Zealand. Methods We analyse up to 1624 bp of mtDNA from 499 'flathead' Galaxias specimens from 145 localities across 14 different river systems. Variation among sampling sites within systems is characterized using ɸ statistics. Results Although similar levels of DNA sequence variation were detected in all rivers sampled, spatial partitioning of this variation was significantly greater within schist (n = 5; mean ɸST = 0.696) than within greywacke (n = 10; mean ɸST = 0.268) rivers. Main conclusions Population connectivity can be strongly influenced by underlying geology, leading to profound differences in the connectivity, phylogeography and diversity of riverine species. [ABSTRACT FROM AUTHOR]

Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag ( Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines. [ABSTRACT FROM AUTHOR]

Aim This study examines beach-cast rafts of Durvillaea antarctica (bull kelp) along New Zealand's east coast to determine spatial variation in beach-cast haplotype assemblages. By using genetic markers, the geographical origins of rafted D. antarctica samples can be determined, allowing for the examination of dispersal pathways, distances rafted, and potential barriers to dispersal. Location An approximately 1000 km stretch of New Zealand's eastern coastline. Methods 686 samples of beach-cast D. antarctica rafts were collected and sequenced for cytochrome c oxidase subunit 1 in order to infer geographical origins and dispersal dynamics of rafted specimens. Results were examined using principal components analysis ( PCA) in order to determine spatial groupings. Analysis of molecular variance ( AMOVA) was used to determine statistical support for the detected spatial groups. Results Hierarchical AMOVA revealed three major regional genetic assemblages, which probably reflect broad oceanographic features. In particular, the north-south genetic partitioning in rafted kelp assemblages either side of the Cape Campbell region in central New Zealand closely corresponds to an oceanographically mediated disjunction previously observed in a number of larval-dispersed marine invertebrate taxa. Main conclusions Findings from this study suggest that passively drifting kelp rafts and planktonic invertebrate larvae may be similarly constrained by oceanographic features, and demonstrate how the phylogenetic structure present in populations of D. antarctica provide a framework with which to map dispersal patterns. [ABSTRACT FROM AUTHOR]

Aim Historical connectivity between drainages may represent an underappreciated contributor to the biodiversity within a catchment. First, we tested whether an isolated population of freshwater-limited galaxiids represents a contribution by past interdrainage connectivity to this system's biodiversity, rather than reflecting intracatchment dispersal or speciation. Second, we sought to distinguish between possible geomorphic processes that could have allowed any past connectivity. Location The Clutha and adjacent Southland region drainages on the South Island of New Zealand. Methods We estimated the phylogeographical relationships among 466 cytochrome b sequences from 'roundhead' Galaxias populations throughout the Southland region and the Clutha drainage, using three different methods. Subsequently, possible geomorphic mechanisms of interdrainage connectivity were examined concurrently with genetic population divergence time estimates obtained by coalescent analysis. Results All samples obtained in the lower Clutha system were genetically attributable to G. gollumoides and reflected at least a third, independent colonization event from Southland involving this species, rather than intradrainage dispersal or speciation by pre-existing Clutha populations. Geomorphological inferences and divergence time estimates of less than 7 ka are consistent with headwater connections across low divides between the lower Clutha and the Catlins region of Southland, rather than anastomosing of main channels during low sea stands. Main conclusions The observation of at least three interdrainage connectivity events influencing the diversity and distribution of G. gollumoides lineages within the Clutha system highlights the potential significance of these processes as contributors to the magnitude and distribution of biodiversity within catchments. [ABSTRACT FROM AUTHOR]

New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades. [ABSTRACT FROM AUTHOR]

Wing reduction and flightlessness are common features of alpine and subalpine insects, and are typically interpreted as evolutionary adaptations to increase fecundity and promote local recruitment. Here, we assess the impact of wing reduction on dispersal in stoneflies (Plecoptera: Gripopterygidae: Zelandoperla) in southern New Zealand. Specifically, we present comparative phylogeographic analyses (COI; H3) of strong-flying Zelandoperla decorata (144 individuals, 63 localities) vs. the co-distributed but weak-flying Zelandoperla fenestrata species group (186 individuals, 81 localities). The latter group exhibits a variety of morphotypes, ranging from fully winged to completely wingless. Consistent with its capacity for strong flight-mediated dispersal, Z. decorata exhibited no substantial phylogeographic differentiation across its broad South Island range. Conversely the weak-flying fenestrata species group exhibited substantial genetic structure across both fine and broad geographic scales. Intriguingly, the variable degrees of wing development observed within the fenestrata species group had no apparent impact on levels of phylogeographic structure, which were high regardless of morphotype, suggesting that even fully winged specimens of this group do not fly. This finding implies that Zelandoperla flight loss occurs independently of wing loss, and might reflect underlying flight muscle reduction. [ABSTRACT FROM AUTHOR]

The evolutionary effects of Southern Hemisphere Pleistocene oceanographic conditions — marked by fluctuations in sea levels and water temperatures, and redirected currents — are poorly understood. The southeastern tip of Australia presents an intriguing model system for studying the biological impacts of palaeoceanography. In particular, contrasting oceanographic conditions that existed on eastern vs. western sides of the Bassian Isthmus during Pleistocene glacial periods allow for natural comparisons between putative refugial vs. re-invading populations. Whereas many western Tasmanian marine taxa were likely eliminated by cold subantarctic water during the last glacial period, eastern Tasmanian populations would have persisted in relatively warm temperatures mediated by the ongoing influence of the East Australian Current (EAC). Here we test for the effects of contrasting palaeoceanographic conditions on endemic bull kelp, Durvillaea potatorum, using DNA sequence analysis (COI; rbcL) of more than 100 individuals from 14 localities in southeastern Australia. Phylogenetic reconstructions reveal a deep (maximum divergence 4.7%) genetic split within D. potatorum, corresponding to the ‘eastern’ and ‘western’ geographical regions delimited by the Bassian Isthmus, a vicariant barrier during low Pleistocene sea levels. Concordant with the western region's cold glacial conditions, samples from western Tasmania and western Victoria are genetically monomorphic, suggesting postglacial expansion from a mainland refugium. Eastern samples, in contrast, comprise distinct regional haplogroups, suggesting the species persisted in eastern Tasmania throughout recent glacial periods. The deep east–west divergence seems consistent with earlier reports of morphological differences between ‘western’ and ‘eastern’ D. potatorum, and it seems likely that these forms represent reproductively isolated species. [ABSTRACT FROM AUTHOR]

Many macroalgae exhibit considerable intraspecific morphological variation, but whether such variation reflects phenotypic plasticity or underlying genetic differences is often poorly understood. We quantified both morphological and genetic variation of 96 plants from seven field sites across eastern South Island, New Zealand, to assess genetic differences between morphotypes of the southern bull kelp Durvillaea antarctica (Cham.) Har. Consistent DNA sequence differentiation across mitochondrial, plastid, and nuclear loci was correlated with two broadly sympatric morphotypes: “cape” and “thonged.” These ecologically, morphologically, and genetically distinct bull-kelp lineages were previously considered to be environmentally determined phenotypes with no underlying genetic basis. Interestingly, the sheltered “cape” lineage appears essentially genetically uniform across its South Island range, whereas the exposed “thonged” lineage exhibits marked phylogeographic structure across its range. Results suggest that D. antarctica in New Zealand comprises two reproductively isolated species. [ABSTRACT FROM AUTHOR]

1. The biological impact of glaciation in Southern Hemisphere freshwaters is poorly understood. Several large rivers of eastern South Island, New Zealand, represent a mosaic of glaciated and non-glaciated regions, and are thus well-suited for studies of post-glacial recolonization. 2. We conducted mtDNA analyses of South Island's endemic non-migratory longjaw galaxiids Galaxias prognathus and G. cobitinis (Osmeriformes: Galaxiidae) to test hypotheses of post-glacial recolonization, and to assess the vicariant effects of Pleistocene mountain building. 3. We analysed the phylogeography of longjaw cytochrome b sequences from 38 sites in central South Island ( n = 83). On the basis of our sampling it seems that G. prognathus and G. cobitinis have a parapatric distribution in the Waitaki River system, their disjunction broadly coinciding with three large post-glacial lakes. Waitaki clades of both species are deeply divergent relative to conspecific taxa in drainages to the north and south. 4. Tests for recent population growth – predicted under post-glacial expansion of G. prognathus– do not refute recent recolonization of streams above glaciated lakes in the Waitaki River drainage. The apparent absence of potential ‘source’ populations from non-glaciated regions suggests a post-glacial population decline for G. prognathus below the Waitaki lakes. 5. Molecular clock calibrations based on several freshwater vicariant events elsewhere in New Zealand supported the geologically-derived hypothesis of Waitaki–Canterbury drainage isolation approximately 300 ka. [ABSTRACT FROM AUTHOR]

We used mtDNA and isozyme analysis of a freshwater fish, Galaxias divergens (Osmeriformes: Galaxiidae), to test a hypothesis of drainage evolution in South Island, New Zealand. Geological evidence indicates that the presently north-flowing Kaituna River branch of the Pelorus River system once flowed south into the Wairau River system. The subsequent flow-reversal is thought to have resulted from Pleistocene subsidence in central New Zealand. mtDNA sequence data corroborated this geological hypothesis: rivers draining into Pelorus Sound were found to retain a genetic lineage of G. divergens that is otherwise restricted to the Wairau River system and adjacent coastal drainages (based on current sampling). Other sampled drainages in northern South Island and southern North Island were found to house lineages that were highly divergent from the Wairau–Pelorus clade. Isozyme data yielded groupings based on fixed differences that were largely congruent with mtDNA clades. Standard molecular calibrations suggest that vicariant isolation of Pelorus and Wairau systems (drainage reversal) occurred in the mid-Pleistocene rather than the late Pleistocene as suggested by geology. Future multidisciplinary analyses will aim to improve our understanding of geological and molecular evolutionary rates. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88, 367–376. [ABSTRACT FROM AUTHOR]

Presents a study which used phylogeographic analysis of mitochondrial DNA of the freshwater Galaxias vulgaris complex to test a geological hypothesis of drainage evolution in South Island, New Zealand. Materials and methods; Results; Discussion.

Abstract We used DNA analysis of galaxiid fish to test a hypothesis of localized headwater capture in South Island, New Zealand. The restricted western, but widespread eastern, distributions of three nonmigratory freshwater fish species suggest that part of the east-flowing Waiau River has been captured by the west-flowing Buller River. However, mitochondrial control region (Kimura 2-parameter distance = 4.1–5.4%) and microsatellite flanking sequences do not support a relationship between Waiau (N = 4 fish sequences) and western populations (N = 8) of Galaxias vulgaris. Instead, the point of capture is probably to the north-east, perhaps the Nelson lakes region. Phylogenetic analysis indicates that western populations, along with populations in the north-east (N = 18), represent a previously unidentified monophyletic Evolutionarily Significant Unit, possibly a cryptic species. We suggest a general caveat for zoogeographic conclusions based on distributional data alone. [ABSTRACT FROM AUTHOR]

Geological processes can strongly affect the distribution and diversification of freshwater-limited species. In particular, a combination of geological and biological data has suggested that Earth history processes can drive vicariant isolation and speciation in non-migratory freshwater fishes. Here, we synthesise recently published geological and freshwater phylogeographic data to illustrate that changes in river drainage geometry are important drivers of galaxiid diversification, both in New Zealand and elsewhere. Major river capture events have led to the isolation and divergence of unique and geographically-restricted lineages, including taxa that are now of prime conservation concern. The parallel phylogeographic effects of drainage shifts have been verified by observations of concordant patterns in co-distributed species. Broadly, this study highlights the dynamic interplay between physical and biological processes in geologically active settings. [ABSTRACT FROM AUTHOR]

Genetic analyses can reveal a wealth of hitherto undiscovered cryptic biodiversity. For co-occurring and morphologically similar species, the combination of molecular, ecological and morphological analyses provides an excellent opportunity for understanding some of the processes that can lead to divergence and speciation. The Australian endemic brown macroalga Durvillaea potatorum (Phaeophyceae) was examined with a combination of genetic and morphological approaches to confirm the presence of two separate species and to infer the processes that led to their divergence. A total of 331 individuals from 11 sites around coastal Tasmania were collected and measured in situ for a range of morphological and ecological characteristics. Tissue samples were also collected for each individual to allow genetic analyses using mitochondrial (COI) and nuclear (28S) markers. Genetic analyses confirmed the presence of two deeply divergent clades. The significant morphological differentiation, despite high levels of intra-lineage variability, further supported their recognition as distinct species. We describe a new species, D. amatheiae sp. nov., which is characterised by a narrower and proportionately shorter stipe, shorter total length, and higher number of stipitate lateral blades and branches than D. potatorum (sensu stricto) . The occurrence of both species in sympatry along Tasmania’s eastern and western coasts, as well as their contrasting patterns of haplotype diversity, supports a hypothesis of geographical isolation, allopatric speciation and subsequent secondary contact in response to sea level and ocean current change throughout the Pleistocene glaciation cycles. This research contributes to resolving the phylogenetic relationships, taxonomy and evolution of the ecologically keystone kelp genus Durvillaea . [ABSTRACT FROM AUTHOR]

New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades. [ABSTRACT FROM AUTHOR]