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Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations
Abstract
While terrestrial megafaunal extinctions have been well-characterised worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450-1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to over-hunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline. This article is protected by copyright. All rights reserved.
... Zealand's biota has experienced a well-documented decline that is clearly associated with human activities (Worthy 1999, Worthy andHoldaway, 2002) over a period of relative climatic stability (Wanner et al., 2008;Rawlence et al., 2016;Waters et al., 2017). As a result of hunting (Rawlence et al., 2015a), rapid landscape modification (McWethy et al., 2010) and the introduction of exotic species that followed both colonisation events, a substantial proportion of New Zealand's endemic vertebrates have become extinct. ...
... Recently, a number of studies have combined ancient and contemporary DNA with morphological analyses and radiocarbon dating, to explore the impact of human settlement on population size in a range of New Zealand animal taxa (see , including sea lions (Phocarctos hookeri; Collins et al., 2014;Rawlence et al., 2016), fur seals (Arctocephalus spp; Salis et al., 2016), kiwi (Apteryx spp; Shepherd and Lambert, 2008;Shepherd et al., 2012), swans (Cygnus spp; Rawlence et al., 2017a), kākāpō (Strigops habroptilus; Bergner et al., 2016;Dussex et al., 2018), kea (Nestor notabilis; Dussex et al., 2015), shags (Leucocarbo spp; Rawlence et al., 2015bRawlence et al., , 2017b and penguins (Megadyptes and Eudyptula spp.; Boessenkool et al., 2009;Rawlence et al., 2015a;Grosser et al., 2015Grosser et al., , 2016Grosser et al., , 2017. Several of these analyses have discovered cryptic extinctions and population declines in coastal and marine fauna following human settlement, and subsequent range expansions of congeneric species. ...
... Phocarctos and Leucocarbo extinctions [Boessenkool et al., 2009;Collins et al., 2014;Rawlence et al., 2015aRawlence et al., , 2016Rawlence et al., , 2018). It is unclear, however, whether these unique Eudyptes specimens represented a mainland breeding colony (e.g. from northern South Island or the lower North Island), or were vagrants from elsewhere. ...
Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as ‘Eudyptes spp.’, we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.
... Ancient-DNA analysis was used to genetically assign ancient Phocarctos specimens to 'subantarctic', 'mainland New Zealand' or 'Chatham Islands' lineages (Collins et al., 2014;Rawlence et al., 2016) (Table S1). Ancient DNA extractions and PCR set-up were carried out in a purpose-built ancient DNA laboratory physically isolated from other molecular laboratories (Knapp et al., 2012): the Otago Palaeogenetics Laboratory at the University of Otago. ...
... A new synthesis of radiocarbon and ancient DNA data suggests synchronous turnover events for Megadyptes penguins (Fig. 2) and Phocarctos sea lions (Fig. 3) at c. 1500 AD. In addition to genetic data from 185 previously sequenced ancient specimens (Boessenkool et al., 2009;Collins et al., 2014;Rawlence et al., 2016), new sequences recovered from 28 additional archaeological Phocarctos specimens revealed clear lineage turnover closely corresponding to the transition between early prehistoric (1280-1450 AD) and middle-to late-prehistoric (1450-1796 AD) periods (Fig. 3). Phylogenetic analyses combining genetic data from these archaeological samples with previously published sequences confirmed their placement into previously described subantarctic and mainland clades (Fig. S1 in Appendix S1). ...
... Additionally, as the prehistoric subantarctic 'source' populations of both Megadyptes and Phocarctos were substantial [long-term N c of P. hookeri 'subantarctic' estimated to be c. 40,000-100,000 individuals Rawlence et al., 2016)], we infer that they likely produced sufficient numbers of vagrants to facilitate rapid northward expansion at this time (Boessenkool et al., 2009;Rawlence et al., 2015a). In contrast to mainland lineage turnover around the onset of the LIA, there is no Biologists and archaeologists have long been intrigued by the biodiversity impacts of Polynesian colonization of the Pacific (Duncan et al., 2013). ...
Aim
To test for simultaneous Holocene biogeographic turnover events in the New Zealand region. Specifically, we synthesize ancient DNA , radiocarbon data and archaeological data to assess the chronologies of late Holocene lineage extinction and replacement.
Location
Cool‐temperate coastal ecosystems of New Zealand and the subantarctic.
Methods
We present new ancient DNA and radiocarbon data for New Zealand sea lions, and synthesize existing climatic, genetic and archaeological data, to test for synchronous megafaunal extinction and replacement events. The collated data include ancient DNA sequences from over 200 ancient sea lion and penguin specimens, in addition to 150 modern genetic samples.
Results
Our temporal genetic analyses show that, following human‐driven extinction events, synchronous marine megafaunal replacement events occurred at around 1500 AD , coinciding with the Little Ice Age onset and an associated drastic human demographic decline in southern New Zealand.
Conclusions
A combination of climatic and human demographic shifts likely facilitated northward expansion of subantarctic sea lion and penguin lineages, replacing extirpated mainland New Zealand marine megafauna. Broadly, the interaction between human pressure and late Holocene climatic change may explain multiple biological turnover events in the Southern Hemisphere.
... If a female sea lion is killed, it's unborn and dependant pups will also die. Modelling shows these slow-breeding pinnipeds could not withstand even low levels of subsistence hunting or predation resulting in their rapid extinction (Rawlence et al., 2016a;Waters et al., 2017). ...
... It may have been more energetically efficient for smaller kurī to hunt these prey than humans, and in turn, they would obtain a greater nutritional benefit in terms of relative body size than larger humans. Archaeological evidence from faunal remains certainly suggests Māori hunted the entire ontogenetic size range of sea lions (Rawlence et al., 2016a), and may have utilised kurī for assistance. Indeed, there is ethnographic evidence dating from the second-half of the nineteenth century for the use of dogs to hunt ground birds in New Zealand (e.g., weka, pūkeko, kākāpō;Beattie, 1920Beattie, , 1939 but the antiquity of this practice is not clear. ...
The pre-human Aotearoa New Zealand fauna was dominated by avian and reptilian species. Prior to first human settlement by East Polynesian colonists, the top predators were two giant raptorial birds. Aside from humans themselves, colonisation also resulted in the simultaneous introduction of two novel mammalian predators into this naive ecosystem, the kiore (Pacific rat) and kurī (Polynesian dog). While the ecological impacts of kiore are relatively well understood, those of kurī are difficult to assess, and as such kurī have frequently been disregarded as having any meaningful impact on New Zealand’s biodiversity. Here we use the archaeological and palaeoecological record to reassess the potential impacts of kurī on this ecosystem. We argue that far from being confined to villages, kurī could have had a significant widespread but relatively localised impact on New Zealand’s avian, reptilian and marine mammal (seals and sea lions) fauna as a novel predator of medium-sized species. In this way, kurī potentially amplified the already significant impacts of Polynesian colonists and their descendants on New Zealand’s ecosystem, prior to European arrival. As such, kurī should be included in models of human impact in addition to over-hunting, environmental modification and predation by kiore.
... Moreover, mitochondrial genomes sequenced from prehistoric (AD 1450-1650) bones of P. hookeri from the Chatham Islands revealed that there was another large population of a sea lion lineage unique to the Chatham Islands (P. hookeri 'Chathams') at the time of Polynesian arrival (Collins, Rawlence, Prost, et al. 2014;Rawlence et al. 2016). This population was driven to extinction within 200 years, again probably due to over-hunting (Collins, Rawlence, Prost, et al. 2014;Rawlence et al. 2016). ...
... hookeri 'Chathams') at the time of Polynesian arrival (Collins, Rawlence, Prost, et al. 2014;Rawlence et al. 2016). This population was driven to extinction within 200 years, again probably due to over-hunting (Collins, Rawlence, Prost, et al. 2014;Rawlence et al. 2016). Current surviving Phocarctos are thus remnants of a once more diverse and widespread sea lion clade. ...
In the 25 years since the first DNA sequences were obtained from the extinct moa, ancient DNA analyses have significantly advanced our understanding of New Zealand's unique fauna. Here, we review how DNA extracted from ancient faunal remains has provided new insights into the evolutionary histories and phylogenetic relationships of New Zealand animals, and the impacts of human activities upon their populations. Moreover, we review how ancient DNA has played a key role in improving our ability to taxonomically identify fragmentary animal remains, determine biological function within extinct species, reconstruct past faunas and communities based on DNA preserved in sediments, resolve aspects of the ecology of extinct animals and characterising prehistoric parasite faunas. As ancient DNA analyses continue to become increasingly applied, and sequencing technologies continue to improve, the next 25 years promises to provide many more exciting new insights and discoveries about New Zealand's unique fauna.
... maui Baker Smith & Pichler, 2002, now inhabiting the coastal waters of the South Island and those of the western North Island, respectively. All three are thought to have been more abundant in the past, with P. hookeri formerly comprising distinct populations in mainland, Chatham Islands and Subantarctic New Zealand regions (Collins et al. 2014;Rawlence et al. 2016). ...
Aotearoa New Zealand today is home to nine extant species of pinniped (seals and sea lions) and 45 cetaceans (whales and dolphins), many of which are globally rare (Table 25.1; Figs 25.1, 25.2). This is slightly more than the eight pinnipeds and 43 cetaceans listed in King et al. (2009), with new discoveries like Ramari’s beaked whale, Mesoplodon eueu Carroll et al., 2021, continuing to add to this diverse local fauna. New Zealand’s marine mammal fossil assemblage is equally rich and has increased by twelve species since King et al. (2009), with a further four having been reassigned to new genera. There is enormous potential for further fossil discoveries, with research so far having focused largely on the upper Oligocene (28–23 million years ago) of the southeastern South Island. The lists of New Zealand extant and fossil marine mammals reported by King et al. (2009) are reviewed here, and updated checklists are provided.
... Multiple life history traits such as flightlessness and large body size increase the extinction risk of takahē/moho (Garcia-Ramirez & Di Marco, 2020). Indeed, modelling analyses have suggested that even low levels of human pressure may have been sufficient to cause the extinction of several large vertebrate taxa in New Zealand (Holdaway et al., 2014;Rawlence et al., 2016). In contrast to the sustained human population pressure in the North Island that likely led to the extinction of moho, the reduced human pressure in the southern South Island (Waters et al., 2017) apparently allowed takahē to persist as a small isolated population in the remote, mountainous relict distribution in Fiordland (e.g. ...
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.
... The arrival of Polynesians in Aotearoa New Zealand around 1280 AD (Wilmshurst et al., 2008), followed later by Europeans (effectively the late 1700s), resulted in widespread species extinctions and habitat modification (Tennyson & Martinson, 2007;McWethy et al., 2014;Rawlence et al., 2020). Since human arrival, at least 70 species of birds have gone extinct, in addition to one mammal (Rawlence et al., 2016;Rawlence et al., 2020), one lizard (Worthy, 1987), and three frogs (Easton et al., 2021). The New Zealand grayling Prototroctes oxyrhynchus (or upokororo) is the only freshwater fish species known to have become extinct in New Zealand (Figure 1), with the last confirmed sighting in 1923 by the anthropologist Te Rangi Hīroa (Sir Peter Henry Buck), who captured "over forty grayling in a funnel-shaped" net in the Waipu River in northern New Zealand (Hīroa, 1926). ...
The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in Aotearoa New Zealand—including the number of colonisation events, the directionality and timing of dispersal, and their relationship to the Australian grayling—is poorly understood. The New Zealand grayling ( Prototroctes oxyrhynchus ) is the only known freshwater fish species to have gone extinct since human arrival in New Zealand. Despite its historical abundance, only 23 formalin-fixed specimens (both wet and dried) exist in museum collections globally, which were previously non-amenable to palaeogenetic analysis.
Here, we used high-throughput DNA sequencing techniques, specifically designed for formalin-fixed specimens, to generate mitochondrial genomes of P. oxyrhynchus , and analysed these within a temporal phylogenetic framework of retropinnid and osmerid taxa.
We recovered strong evidence for a sister relationship between the New Zealand and Australian grayling ( P. mareana ), with the two having a common ancestor around 13.8 Mya (95% HPD: 6.1–23.2 Mya), after the height of Oligocene marine inundation in New Zealand.
Our temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance.
This study provides further insights into the possible drivers of the extinction of the New Zealand grayling, and highlights how advancements in palaeogenetic techniques can be used to test evolutionary hypotheses in extinct (and living) fish, which have been comparatively neglected in the field of ancient DNA.
... Worthy 1987Worthy , 1991Worthy and Holdaway 2002;Tennyson and Martinson 2006). Combined palaeogenetic and morphological reanalyses have (1) allowed taxonomic identifications based on morphology to be tested, resulting in the recent description of several new extinct species of penguin (Boessenkool et al. 2009;Cole et al. 2019); shag ( Figure 2D; Rawlence, Till, et al. 2017), swan ( Figure 2E; Rawlence, Kardamaki, et al. 2017), and petrel , and new genetic lineages of rāpoka sea lion ( Figure 2F; Collins et al. 2014;Rawlence et al. 2016); and (2) the provenance of historical museum specimens, which often underlie our understanding of the severity of human impact, to be verified (e.g. Boessenkool et al. 2010;Shepherd et al. 2013;Rawlence, Kennedy, et al. 2014;Verry et al. 2019;Mudge et al. 2022;Scofield et al. 2021). ...
Thirty years ago, DNA sequences were obtained from an extinct Aotearoa New Zealand animal for the first time. Since then, ancient DNA research has provided many–often unexpected–insights into the origins of New Zealand’s terrestrial and marine vertebrate fauna. Because recent human activities in New Zealand have caused the decline or extinction of many endemic plant, bird, reptile, and marine mammal species, ancient DNA has been instrumental in reconstructing their identities and origins. However, most ancient DNA studies focusing on New Zealand species have been restricted to vertebrates, with small sample sizes, and/or relatively few genetic markers. This has limited their power to infer fine-scale biogeographic patterns, including (pre)historic distributions and range-shifts driven by past climate and environmental change. Recently, ‘next-generation’ methodological and technological advances have broadened the range of hypotheses that can feasibly be tested with ancient DNA. These advances represent an exciting opportunity for further exploring New Zealand biogeography using ancient DNA, but their promise has not yet been fully realised. In this review, we summarise the last 30 years of ancient DNA research into New Zealand faunal biogeography and highlight key objectives, challenges, and possibilities for the next 30 years and beyond.
... Ancient DNA can provide a useful tool for conservation managers as knowledge of past genetic diversity, geographic range expansions/contractions and the factors that lead to population declines or extinctions is important for informing management decisions(Leonard 2008;Grealy et al. 2017). Much of Aotearoa New Zealand's endemic biota has been driven to extinction or reduced to relictual distributions following human arrival, and so aDNA provides a means to examine the genetic composition of such species prior to anthropogenic impacts.Examples of the use of aDNA to inform the conservation and management of endemic Aotearoa New Zealand species includes quantifying temporal declines in genetic diversity(Grueber & Jamieson 2008;Tracy & Jamieson 2011;Dussex et al. 2015;Bergner et al. 2016), determining the origin of contemporary genetic structure(Tracy & Jamieson 2011), clarifying past distribution of species and populations/genetic lineages(Shepherd & Lambert 2008;Wilmshurst et al. 2014;Verry et al. 2019; Scarsbrook et al. 2021), and characterizing unsustainable harvesting rates that have driven species towards extinction(Rawlence et al. 2016). ...
1. To achieve the vision outlined in the national strategy for biodiversity, Te Mana o te Taiao, we will need to unite diverse disciplines, including conservation genetics/genomics.
2. As conservation genetic/genomic data generated for—and associated with—taonga (treasured) species is also taonga, we highlight the need for collaborative research partnerships that centre the needs, aspirations and expertise of mana whenua.
3. As a team of predominantly early-career conservation genetics and genomics researchers working across institutions as Te Tiriti o Waitangi partners, each speaking to our own expertise, we review available and emerging tools in the conservation genetics/genomics toolbox.
4. To support practitioners in identifying appropriate and affordable tools from the toolbox, we present a table that encompasses resource requirements (including finances, time, and skill) to assist conservation practitioners in assessing the associated costs and benefits of these tools for informing conservation management.
5. To support researchers and practitioners in establishing long-lasting partnerships with mana whenua, we highlight key aspects of data management and data sovereignty for consideration.
6. Intended as a platform to initiate discussion within and among conservation practitioners and researchers, mana whenua, and local communities, the development of government policies is beyond the scope of this contribution.
7. To meet the vision of Te Mana o te Taiao, we conclude by calling for a transdisciplinary approach that includes conservation genetics/genomics.
... Reconstructing historic population genetic diversity and structure from museum specimens has been enhanced through new methods that allow capture and enrichment of highly degraded ancient DNA (Hawkins et al. 2016;Schmid et al. 2017). These types of approaches have been used to examine change in population genetic diversity and differentiation over time in alpine chipmunks (Tamias alpinus) with changing habitat availability (Bi et al. 2013), in social and asocial tucos-tucos (Ctenomys spp.) in response to a volcanic eruption (Hsu et al. 2017), and in the Chatham Island sea lion (Phocarctos hookeri) population in response to human settlement (Rawlence et al. 2016). Quantifying change over time in genomic variation and adaptation is only made possible through the availability of natural history collections of archaeological and historic specimens that allow unparalleled opportunities to understand the ecological and evolutionary implications of global change (Hofman et al. 2015). ...
Genomic technologies have advanced rapidly in recent decades and have ushered in an exciting new era for the study of mammals. Mammalogists working with non-model species are now able to explore many new research areas that were unimaginable only a short time ago. For example, it is currently possible for individual researchers to sequence and assemble genomes for mammalian species of their choosing and to generate genome-wide DNA sequence data from hundreds of individuals simultaneously. Moreover, the miniaturization of both PCR and sequencing technology has created new opportunities for generating real-time DNA or RNA sequence data in the field. Here, we highlight emerging genomic technologies and associated methods that are providing exciting new research avenues for mammalogists in the fields of evolutionary genomics and ecology. Our aim is to not only provide a resource for novel experimental design, but also to provide a record of the current state of genomic applications as the American Society of Mammalogists enters a new century of discovery.
... However, population-level ancient DNA (aDNA) studies using complete mitochondrial genomes (mitogenomes) provides an opportunity to improve our understanding of past ecological and evolutionary processes (Cole & Wood 2018). For example, recent bioheritage research that combines mitogenomes from pre-and post-decline populations has revealed rapid biotic shifts in the distribution of Phocarctos sea lions (Rawlence et al. 2016) and rapid loss of genetic diversity in kākāpō (Dussex et al. 2018). Moreover, mitogenomes recovered from the remains and substrates of extinct species (e.g. ...
In the past few years genetic technologies springing from advances in DNA sequencing (so-called high-throughput sequencing), and/or from CRISPR/Cas9 gene editing, have been proposed as being useful in bioheritage research. The potential scope for the use of these genetic technologies in bioheritage is vast, including enabling the recovery of threatened species, engineering proxies of extinct species and genetically controlling pests. While these technologies are often complex, they provide new opportunities that may help support New Zealand’s beleaguered flora and fauna, and thus warrant scientific examination. Here we discuss these genetic technologies, focussing on scientific benefits and risks of each. We also acknowledge the social, cultural, ethical and regulatory constraints on their use, with emphasis on the importance of partnership with tangata whenua to determine when, whether or how these technologies should be used in enhancing New Zealand’s bioheritage. We hope this will provide source material to support future decision making around the use of new genetic technologies in bioheritage.
... 750 years ago), and the archipelago's naive fauna was subsequently devastated, with at least 58 endemic avian taxa having been driven to extinction over subsequent centuries (Holdaway, Worthy, & Tennyson, 2001;Tennyson & Martinson, 2007;. In addition to the loss of the iconic moa (Worthy & Holdaway, 2002), a number of large coastal bird and pinniped lineages were rapidly eliminated by hunting and later replaced by exotic lineages (e.g., Boessenkool et al., 2009;Collins et al., 2014;Rawlence et al., 2015Rawlence et al., , 2016Waters, Fraser, Maxwell, & Rawlence, 2017). ...
Montano et al.'s (Evolutionary Applications, 2017) recent coalescent analysis of modern black swan (Cygnus atratus) genotypes concluded that New Zealand's native black swan survived prehistoric hunting, to later hybridize with introduced black swans from Australia. However, this persistence scenario conflicts with new ancient DNA, morphometric and archaeological analyses of prehistoric New Zealand swan (C. sumnerensis) remains, which instead support a wholesale extinction-replacement scenario. Multiple lines of evidence indicate that C. sumnerensis did not survive beyond the earliest phase of Polynesian settlement in New Zealand and thus question the reliability of coalescent inferences derived from small numbers of microsatellite loci.
... Yet, the large difference in haplotype composition between archaeological and modern gray seals suggests there may have been a genetically distinct gray seal population off the coast of the Northeast US prior to local extirpation. Furthermore, the low frequency of the central haplotypes in the gray seal network (in contrast to numerically dominant central haplotypes in the harbor seal network, and most star-like networks in the literature) is consistent with the historical loss of a (Collins et al. 2014;Rawlence et al. 2016) and the Canadian Maritimes walrus (Odobenus rosmarus) (McLeod et al. 2014). The loss of a historical gray seal subpopulation may be consistent with their reproductive biology, particularly if they were hunted at or near breeding colonies. ...
Conservation successes of the past several decades provide natural settings to study post-bottleneck evolutionary processes in species undergoing recovery. Here, we study the impact of demographic change on genetic diversity in parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina concolor). We compare genetic diversity at the mitochondrial control region today to diversity in archaeological specimens, which represent the populations prior to the regional bounties of the late 1800s to mid-1900s that drastically reduced population sizes and led to local extirpations. We further assess genetic diversity throughout recovery, using biological collections from ongoing long-term studies of both species. Overall, the genetic data are consistent with the historical presence of large, genetically diverse populations of pinnipeds prior to human exploitation, and suggest that gray seals were more dramatically impacted by historical bottlenecks than harbor seals in the Northwest Atlantic. Current mitochondrial diversity in both species is relatively high, and we observe little change over the past several decades during a period of roughly parallel rapid population increases. However, there remain large differences in haplotype composition between pinniped populations of pre-exploitation and today, a lasting genetic signature of historical exploitation that is likely to persist into the future.
... [54]). As well as wholesale species extinctions, several taxa have experienced substantial anthropogenic range reductions and losses of phylogeographic diversity [55][56][57]. ...
The spread of exotic species represents a major driver of biological change across the planet. While dispersal and colonization are natural biological processes, we suggest that the failure to recognize increasing rates of human-facilitated self-introductions may represent a threat to native lineages. Notably, recent biogeographic analyses have revealed numerous cases of biological range shifts in response to anthropogenic impacts and climate change. In particular, ancient DNA analyses have revealed several cases in which lineages traditionally thought to be long-established "natives" are in fact recent colonizers. Such range expansion events have apparently occurred in response to human-mediated native biodiversity declines and ecosystem change, particularly in recently colonized, isolated ecosystems such as New Zealand. While such events can potentially boost local biodiversity, the spread of exotic lineages may also hasten the decline of indigenous species, so it is essential that conservation managers recognize these rapid biotic shifts. .
This article both introduces our Special Issue on “Zooarchaeology and Human Ecodynamics in East Polynesia” and reviews recent research from East Polynesia at large. The seven articles and discussion essay derive from a symposium at the 14th International Council for Archaeozoology (ICAZ) conference in Cairns, Australia (2023). To contextualize these contributions, we review recent studies (2016–2024) from the region relating to human–animal relationships, including morphological, ancient DNA, and stable isotope research. Seven areas or themes emerge from our review, representing substantive, analytical and technical domains. These include (1) geographic coverage; (2) methodological issues; (3) assessments of anthropogenic impacts; (4) studies of domestic and commensal taxa; (5) animals in social, ritual and symbolic roles; (6) engagement with historical records and traditional ecological knowledges (TEK); and (7) emerging technologies. We conclude with a brief summary of recent achievements and propose future directions for zooarchaeological studies in East Polynesia and the wider Pacific.
The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in New Zealand (NZ), including their relationship to the Australian grayling, is poorly understood. The NZ grayling (Prototroctes oxyrhynchus) is the only known fish in NZ to have gone extinct since human arrival there. Despite its historical abundance, only 23 wet and dried, formalin-fixed specimens exist in museums. We used high-throughput DNA sequencing to generate mitogenomes from formalin-fixed P. oxyrhynchus specimens, and analysed these in a temporal phylogenetic framework of retropinnids and osmerids. We recovered a strong sister-relationship between NZ and Australian grayling (P. mareana), with a common ancestor ~13.8 Mya [95% highest posterior density (HPD): 6.1–23.2 Mya], after the height of Oligocene marine inundation in NZ. Our temporal phylogenetic analysis suggests a single marine dispersal between NZ and Australia, although the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. This study provides further insights into the possible extinction drivers of the NZ grayling, informs discussion regarding reintroduction of Prototroctes to NZ and highlights how advances in palaeogenetics can be used to test evolutionary hypotheses in fish, which, until relatively recently, have been comparatively neglected in ancient-DNA research.
The field of conservation biology has a long history of incorporating diverse disciplines into its ‘toolbox’ for improved outcomes. One such discipline is conservation genomics, which has experienced fast-paced growth and development over the last decade and offers exciting opportunities to help achieve the vision outlined in Aotearoa New Zealand’s national strategy for biodiversity – Te Mana o te Taiao. However, integrating these emerging methodologies into meaningful conservation practice has proven challenging, mostly due to uncertainty around the utility of these data and effective allocation of limited funding. This report addresses these challenges by outlining potential strategies for utilising genetic/genomics in conservation from the perspective of predominantly early-career conservation researchers working as Te Tiriti o Waitangi partners. It is intended to initiate discussion among conservation practitioners and researchers, mana whenua and local communities. To support practitioners in identifying appropriate and cost-effective genetic/genomic tools, their associated costs and benefits for informing conservation management are presented. Because conservation genetic/genomic data generated for – and associated with – taonga (treasured) species are also taonga, the report emphasises the need for collaborative research partnerships that centre the needs, aspirations and expertise of mana whenua, and highlights key aspects of data management and sovereignty. A transdisciplinary approach to conservation that includes genetics/genomics is recommended.
This chapter focuses on the anthropogenic impacts on Aotearoa New Zealand's (NZ) biodiversity up until the early 20th century, from an archaeological, paleoecological and evolutionary perspective. Palynology and charcoal analysis have been the main methods used to study vegetation change through time. Most pollen records are used to investigate natural processes of long‐term, multi‐millennial paleoenvironmental change, addressing various themes especially climate change. These studies can also inform on fire regimes, both locally and nationally; changes in sedimentation regimes; and the timing and impact of human arrival, although anthropogenic changes are often only a small component of this type of research. Given its late settlement, NZ offers a unique opportunity to examine the early stages of cultivation and domestication (e.g. what stage in the domestication process is genetic diversity lost), in conjunction with Māori oral histories, which complement western scientific methods and provide a more complete picture of past translocations.
Chapter 6:
Wonderful life at the South Pole 100 to 90 million years ago—An ancient polar greenhouse ecosystem
New Zealand's endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications. Our analyses show that the King Shag was formerly widespread around southern coasts of the North Island and the northern parts of the South Island but experienced population and lineage extinctions, and range contraction, probably after Polynesian arrival. This history parallels range contractions of other New Zealand seabirds. Conservation management of the King Shag should take into account this species narrow distribution and probable reduced genetic diversity. Moreover, combined genetic, morphometric and osteological analyses of prehistoric material from mainland New Zealand suggest that the now extinct northern New Zealand Leucocarbo populations comprised a unique lineage. Although these distinctive populations were previously assigned to the King Shag (based on morphological similarities and geographic proximity to modern Leucocarbo populations), we herein describe them as a new species, the Kohatu Shag (Leucocarbo septentrionalis). The extinction of this species further highlights the dramatic impacts Polynesians and introduced predators had on New Zealand's coastal and marine biodiversity. The prehistoric presence of at least four species of Leucocarbo shag on mainland NZ further highlights its status as a biodiversity hotspot for Phalacrocoracidae.
The New Zealand sea lion (NZ sea lion), Phocarctos hookeri, is New Zealand G ÇÖs only endemic pinniped, and one of the worlds rarest otariids. It is classified as G ÇÿThreatened G ÇÖ based primarily on the low number of breeding sites and restricted distribution. In New Zealand, a species listed as G Çÿthreatened G ÇÖ is required to be managed to allow its recovery and removal from the list within 20 years. For NZ sea lions this is dependant on the establishment of new breeding areas. However, understanding the recolonisation processes for pinnipeds is still in its infancy with factors such as philopatry needing more research to understand individual dispersal and the recolonisation process. This paper presents the first quantitative investigation into the level of site fidelity and philopatry to breeding beaches in NZ sea lions. Data from resights of NZ sea lions marked as pups from the northern Auckland Island breeding area suggest that both site fidelity and philopatry are important characteristics of this species. Our results show that overall: (1) females have a higher resighting rate than males, particularly at natal sites; (2) female non-natal resightings are predominantly restricted to locations within the northern Auckland Island breeding area (an area of ~10 km2), whereas male resightings are more widely dispersed (up to 700 km to NZ mainland); and (3) philopatry occurs for both sexes, but is more predominant in females than males, with males displaying delay related to sexual and social maturity. The colonisation of new breeding habitats rarely occurs when philopatry is strong and population density is low, stable or declining such as seen for NZ sea lions. Therefore, this research indicates that management of NZ sea lions needs to minimise anthropogenic mortality and encourage population growth to maximise density at breeding sites and encourage females to disperse to establish new breeding areas.
With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
Understanding the life history basis of the population dynamics of threatened species is crucial to their assessment and recovery. Within the Southern Pacific Ocean, the decline and range contraction of New Zealand sea lions (NZSLs) (Phocarctos hookeri) are an exemplary case of a major fisheries and conservation controversy. Despite the use of bycatch reduction measures, the main population of the NZSL has declined since 1998 and its vulnerability to threats is poorly understood. Here we develop a population model for the declining population of the endangered NZSL at the Auckland Islands, New Zealand (50∘30′S,166∘17′E), parameterised by mark-recapture data of 2928 female NZSLs spanning 15 years from 1998 to 2012, and provide the first comprehensive analysis of NZSL population dynamics and its relationship to life history. Our model closely predicts the observed trend in population censuses of the main breeding population. We found that the population will continue to decline without effective intervention. Furthermore, we found that the population growth rate is most responsive to changes in survival of adult female NZSLs—the demographic group that is most threatened by fishery bycatch. Nevertheless, inferences about the efficacy of NZSL bycatch reduction measures are still imprecise. Combined, this could explain why the main population of NZSLs continues to decline. Our results emphasise that reliable data on bycatch reduction measures are needed, if they are to be shown to protect key demographic groups of marine mammals.
Archaeological research in the Auckland Islands, south of New Zealand, has disclosed earth ovens, middens and flaked stone tools dating to the thirteenth-fourteenth centuries AD. This is the first site of prehistoric settlement in the outlying islands of the Subantarctic. Polynesians and their dogs survived on seals and seabirds for at least one summer. The new data complete a survey of colonisation in the outlying archipelagos of South Polynesia and show that it occurred contemporaneously, rapidly and in all directions from mainland New Zealand.
This paper provides an overview of the contentious issue of global megafaunal extinctions in the Late Quaternary. The main proposed causes are ‘overkill’, environmental change or a combination of both. There are major objections to the other suggested causes. Extinctions were highly variable in their severity between different zoogeographical regions, with the greatest impact in North America, South America and Australia, but also substantial in northern Eurasia. Sub-Saharan Africa and Southern Asia were much less affected. For northern Eurasia, detailed chronologies show a staggered extinction pattern, in which each megafaunal species exhibits unique and complex distributional shifts, culminating in extinction for some species and survival in others. Environmental drivers were clearly very important, although the possible role of humans is not yet clear. Alaska/Yukon also has a good radiocarbon record which also suggests a staggered extinction pattern. However, the available data for the rest of North America are largely unsatisfactory. South America also boasted spectacular extinct megafauna, but again the currently available dates are insufficient to reliably discern patterns or possible causes. Australia and New Guinea also suffered major losses, but extinctions probably occurred much earlier than elsewhere, so that establishing a chronology is especially difficult. Africa and Southern Asia have the least available data. In order to make meaningful progress, it is vital to establish a large database of reliable radiocarbon dates for each region made directly on securely identified megafaunal remains. The need is for much more high quality data, not more debate based on imperfect evidence. Copyright © 2014 John Wiley & Sons, Ltd.
The thickness and weight of skin, blubber, and body core were measured from 12 dead Steller sea lion pups (Eumetopias jubatus). These necropsied pups represented a wide range of body sizes and conditions (small to large, and fat to no-fat), and were chosen to compare the relative body con-ditions of healthy and starved pups. Seven of the pups lacked blubber and were significantly lighter for a given length compared to the five that had fat at their time of death. Volume exceeded mass by a factor of 1.3% with density averaging 0.987 g cm 3 . Skin and blubber were not uniformly thick over the body surface. Skin was thinnest on the head and around the flippers (3 mm), and became thicker towards the rump (5 mm). Skin thickness did not differ between dorsal and ventral sides, unlike blubber, which was thickest on the ventral side, increasing from the snout (1.5 mm) to mid-trunk (7 mm) and decreasing posteriorly (5 mm at the tail). Along the back, blubber increased from 1 mm at the snout to about 4.5 mm at mid-trunk. The five pups that died of trauma had about 13% skin and 10% blubber (expressed as a proportion of total body mass). Starvelings lost an estimated 43% of their body mass before dying (10% blubber, and 33% body core). Morphometric measurements applied to three proposed indices of body con-dition suggest that girth is not a good predictor of body condition for Steller sea lion pups. Only the ratio of observed to predicted body mass derived from standardized mass-length relationships could distinguish starvelings from pups with body fat.
Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction-replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction.
Tipping points ? where systems shift radically and potentially irreversibly into a different state ? have received considerable attention in ecology. Although there is convincing evidence that human drivers can cause regime shifts at local and regional scales, the increasingly invoked concept of planetary scale tipping points in the terrestrial biosphere remains unconfirmed. By evaluating potential mechanisms and drivers, we conclude that spatial heterogeneity in drivers and responses, and lack of strong continental interconnectivity, probably induce relatively smooth changes at the global scale, without an expectation of marked tipping patterns. This implies that identifying critical points along global continua of drivers might be unfeasible and that characterizing global biotic change with single aggregates is inapt.
When did cattle come to South Africa? Radiocarbon dates on a newly found cow horn indicates a time in the early first millennium AD. In a study of the likely context for the advent of cattle herding, the authors favour immigrants moving along a western route through Namibia.
We introduce the weighted likelihood bootstrap (WLB) as a way to simulate approximately from a posterior distribution. This method is often easy to implement, requiring only an algorithm for calculating the maximum likelihood estimator, such as iteratively reweighted least squares. In the generic weighting scheme, the WLB is first order correct under quite general conditions. Inaccuracies can be removed by using the WLB as a source of samples in the sampling-importance resampling (SIR) algorithm, which also allows incorporation of particular prior information. The SIR- adjusted WLB can be a competitive alternative to other integration methods in certain models. Asymptotic expansions elucidate the second- order properties of the WLB, which is a generalization of Rubin’s Bayesian bootstrap [D. B. Rubin, Ann. Stat. 9, 130-134 (1981)]. The calculation of approximate Bayes factors for model comparison is also considered. We note that, given a sample simulated from the posterior distribution, the required marginal likelihood may be simulation consistently estimated by the harmonic mean of the associated likelihood values; a modification of this estimator that avoids instability is also noted. These methods provide simple ways of calculating approximate Bayes factors and posterior model probabilities for a very wide class of models.
The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.
The estimation of life-history parameters for a threatened species is important for understanding its biology and helping to determine management options. This research investigates age- and sex-related survival estimates incorporating tag loss for New Zealand (NZ) sea lions (Phocarctos hookeri) from Sandy Bay, Enderby Island, Auckland Islands, New Zealand, using multistate mark–recapture data from known-age individuals over 8 years (1997–1998 to 2005–2006). Survival estimates and tag loss rates differed significantly by sex and age class, with adult males having the lowest tag retention of any age or sex class and females ≥ 3 years old having lower survival estimates than their male counterparts. The variability and lower female survival relative to males is a critical problem for NZ sea lions, because even small changes in adult female survival significantly affect population trends for such large, long-lived mammals.
Context. Handling animals is essential for many applications in wildlife management. However, currently there are limited techniques to safely handle and move large mobile pinnipeds, particularly when they cannot be physically restrained first. Such animals can be the cause of many land-based wildlife–human conflicts. The New Zealand (NZ) sea lion (Phocarctos hookeri) is the world's rarest and second largest otariid, and is in severe decline. Although most NZ sea lions live on uninhabited NZ subantarctic islands, a small population is recolonising the coastline of Otago, NZ and this close proximity with humans can cause conflict. Aims. The aim of this research was to assess a method of remote chemical anaesthesia for its ability to safely and practically immobilise large pinnipeds to allow attachment of satellite tracking equipment and to handle and potentially move animals if in situations of conflict. Methods. The chemical anaesthetic Zoletil ® was remotely applied to immobilise adult male NZ sea lions at Enderby Island, Auckland Islands, to allow handling and the application of satellite tracking equipment. Key results. Six adult males weighing up to 330 kg were successfully anaesthetised, weighed and measured. Two of these had satellite location tags attached, which showed two very different post-breeding movement patterns by adult males and indicated minimum overlap with local fisheries activities. Conclusions. This remote anaesthesia technique was successful for adult male NZ sea lions and could be used for the immobilisation and management of other large mobile pinnipeds. Implications. The ability to anaesthetise and safely handle large adult male pinnipeds will provide better management in areas where animals come in close contact with human populations with possible lethal interactions or where attachment of monitoring equipment is required to investigate population parameters or possible lethal interactions.
The New Zealand sea lion (NZ sea lion), Phocarctos hookeri, is New Zealand's only endemic pinniped, and one of the worlds rarest otariids. It is classified as 'Threatened' based primarily on the low number of breeding sites and restricted distribution. In New Zealand, a species listed as 'threatened' is required to be managed to allow its recovery and removal from the list within 20 years. For NZ sea lions this is dependant on the establishment of new breeding areas. However, understanding the recolonisation processes for pinnipeds is still in its infancy with factors such as philopatry needing more research to understand individual dispersal and the recolonisation process. This paper presents the first quantitative investigation into the level of site fidelity and philopatry to breeding beaches in NZ sea lions. Data from resights of NZ sea lions marked as pups from the northern Auckland Island breeding area suggest that both site fidelity and philo-patry are important characteristics of this species. Our results show that overall: (1) females have a higher resighting rate than males, particularly at natal sites; (2) female non-natal resightings are predominantly restricted to locations within the northern Auckland Island breeding area (an area of ~10 km 2), whereas male resightings are more widely dispersed (up to 700 km to NZ mainland); and (3) philopatry occurs for both sexes, but is more predominant in females than males, with males displaying delay related to sexual and social maturity. The colonisation of new breeding habitats rarely occurs when philopatry is strong and population density is low, stable or declining such as seen for NZ sea lions. Therefore, this research indicates that management of NZ sea lions needs to minimise anthropogenic mortality and encourage population growth to maximise density at breeding sites and encourage females to disperse to establish new breeding areas.
1. The New Zealand (NZ) sea lion Phocarctos hookeri is NZ's only endemic pinniped and is listed as 'nationally critical'. The species breeds in the NZ sub-Antarctic: 71% of the population at the Auckland Islands (2010 pup production: 1814 39) and the remaining 29% on Campbell Island (726 pups in 2010). 2. Pup production at the Auckland Islands has declined by 40% since 1998 (1998: 3021 pups produced): only 1501 pups were born in 2009. This decline is directly linked to philopatric females not returning to breeding areas. While the Auckland Island population has declined, the Campbell Island population appears to be increasing slowly. 3. Potential reasons for the decline in the Auckland Island population, but not in the Campbell Island population, include non-anthropogenic factors: (i) disease epizoot-ics, (ii) predation, (iii) permanent dispersal or migration, (iv) environmental change; and anthropogenic impacts: (v) population 'overshoot', (vi) genetic effects, (vii) effects of contaminants, (viii) indirect effects of fisheries (i.e. resource competition) and (ix) direct effects of fisheries (i.e. by-catch deaths). Of the nine potential reasons examined here, six can be discounted (ii–vii). Bacterial epizootics (i) occur in the NZ sea lion population, but their impact has predominantly increased pup mortality, which is unlikely to cause the severe decline observed, as pup mortality throughout the species is naturally high and variable. 4. The most plausible hypotheses, based on available evidence, are that the observed decline, in particular, the decreasing number of breeding females in the Auckland Island population, is caused by (viii) fisheries-induced resource competition and (ix) fisheries-related by-catch. By-catch is the main known anthropogenic cause of mortality in the species. Competition with fisheries resulting in resource compe-tition, nutrient stress and decreased reproductive ability in NZ sea lions should be a priority area for future research.
Dispersal impacts on a range of population parameters making it a key piece of information in species conservation. Despite its importance, dispersal is poorly characterized for many species: pinnipeds are no exception. Understanding dispersal patterns of the New Zealand sea lion Phocarctos hookeri is crucial in the conservation management of the species as its recovery to a non-threatened status hinges on range recolonisation. In this study, we examined the movements of breeding adult male New Zealand sea lions within and following the breeding season of the 2002/03 austral summer using a novel multi colony approach. Based on resightings of 202 individually identifiable adult males, we found (1) a previously unappreciated, high level of dispersal by adult territorial males between breeding colonies during the pupping period and (2) that breeding males disperse to the extremes of the species’ range at the end of female oestrous. Our findings are contrary to the current paradigm of otariid breeding behaviour, which is believed to consist of prolonged, uninterrupted male territoriality based on intense male-male competition and sustained fasting. Adult male dispersal between colonies and across the species range has important implications for adult males as vectors of disease in three recent epizootics, species management and species recovery via recolonisation as males are apparently remaining part of a localized, vulnerable breeding population.
As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Both anthropologists and nutritionists have long recognized that the diets of modern-day hunter-gatherers may represent a reference standard for modern human nutrition and a model for defense against certain diseases of affluence. Because the hunter-gatherer way of life is now probably extinct in its purely un-Westernized form, nutritionists and anthropologists must rely on indirect procedures to reconstruct the traditional diet of preagricultural humans. In this analysis, we incorporate the most recent ethnographic compilation of plant-to-animal economic subsistence patterns of hunter-gatherers to estimate likely dietary macronutrient intakes (% of energy) for environmentally diverse hunter-gatherer populations. Furthermore, we show how differences in the percentage of body fat in prey animals would alter protein intakes in hunter-gatherers and how a maximal protein ceiling influences the selection of other macronutrients. Our analysis showed that whenever and wherever it was ecologically possible, hunter-gatherers consumed high amounts (45-65% of energy) of animal food. Most (73%) of the worldwide hunter-gatherer societies derived >50% (> or =56-65% of energy) of their subsistence from animal foods, whereas only 14% of these societies derived >50% (> or =56-65% of energy) of their subsistence from gathered plant foods. This high reliance on animal-based foods coupled with the relatively low carbohydrate content of wild plant foods produces universally characteristic macronutrient consumption ratios in which protein is elevated (19-35% of energy) at the expense of carbohydrates (22-40% of energy).
The pristine island ecosystems of East Polynesia were among the last places on Earth settled by prehistoric people, and their colonization triggered a devastating transformation. Overhunting contributed to widespread faunal extinctions and the decline of marine megafauna, fires destroyed lowland forests, and the introduction of the omnivorous Pacific rat (Rattus exulans) led to a new wave of predation on the biota. East Polynesian islands preserve exceptionally detailed records of the initial prehistoric impacts on highly vulnerable ecosystems, but nearly all such studies are clouded by persistent controversies over the timing of initial human colonization, which has resulted in proposed settlement chronologies varying from approximately 200 B.C. to 1000 A.D. or younger. Such differences underpin radically divergent interpretations of human dispersal from West Polynesia and of ecological and social transformation in East Polynesia and ultimately obfuscate the timing and patterns of this process. Using New Zealand as an example, we provide a reliable approach for accurately dating initial human colonization on Pacific islands by radiocarbon dating the arrival of the Pacific rat. Radiocarbon dates on distinctive rat-gnawed seeds and rat bones show that the Pacific rat was introduced to both main islands of New Zealand approximately 1280 A.D., a millennium later than previously assumed. This matches with the earliest-dated archaeological sites, human-induced faunal extinctions, and deforestation, implying there was no long period of invisibility in either the archaeological or palaeoecological records.
The Chatham Islands were a challenging environment for East Polynesian colonisers. The successful long term settlement of these islands can be attributed to the first people applying and adapting Polynesian strategies to the colonisation of an unfamiliar environment. Previous studies have suggested that settlement and subsistence practices were entirely focused upon the collection of wild plants and fauna, throughout the Moriori sequence with a heavy dietary reliance on one marine species, the New Zealand fur seal (Arctocephalus forsteri). This interpretation is not consistent with the results of this research.
In this thesis a holistic multi-proxy research design is used to identify terrestrial plant use by Moriori and the landscape modification which is associated with the introduction of East Polynesian subsistence practices. The primary data sets employed are the ethnographic and historical accounts of Moriori subsistence, archaeological investigations of the broad-leaved forests and associated sites, anthracological and palynological analyses to identify past vegetation regimes and the anthropogenic effects, and to date when humans began to modify the environment. The results suggest that after an initial period of rapid population growth, even though marine mammals were still available in large numbers, the first settlers began to modify the environment to increase terrestrial production.
It is argued that the environmental changes occurred in part to increase the productivity of wild plants, particularly bracken fern (Pteridium esculentum). The most important change to the vegetation was the intentional introduction and management of the mainland New Zealand endemic tree Corynocarpus laevigatus. The broad-leaved forests, a previously under-researched component of Moriori subsistence, are shown to have been actively managed by Moriori. They were an integral component of the subsistence practices in the ‘late’, post-1650AD, Moriori sequence. The introduction and cultivation of Corynocarpus laevigatus was essential to the long term colonisation of the Chatham Islands in the absence of the standard tropical East Polynesian cultigens.
We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees-- i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.
Orthodox reconstructions of subsistence and settlement patterns on Chatham Island proposed that throughout the pre-contact period, Moriori lived within small home ranges and relied for food predominantly on fur seals, with plant foods being of little importance. Reassessment of the Point Durham sites on which these reconstructions were based demonstrates that they were not contemporary, which undermines the orthodox model. Chronological evidence indicates two phases of pre-contact occupation and that the largest fur seal midden probably derives from the early historical period. During both pre-contact phases, settlement patterns involved residential mobility between sites of different function along with the transporting of resources over wider territories than the orthodox model allowed. Subsistence evidence shows a shift from initial reliance on fur seals to a broader spectrum of smaller marine animals. Furthermore, new palaeobotanical data indicate that plants, in particular kōpi (Corynocarpus laevigatus), were an important component of diet.
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 southern-most (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 versus stability) reflect differential human impacts in mainland South Island versus Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
Pup production of the ‘nationally critical’ New Zealand sea lion Phocarctos hookeri has declined by 48 % since 1998, with fisheries bycatch playing a role in this decline. Current management of the sea lion population involves, amongst other measures, the setting of an annual bycatch limit based on Bayesian modelling of the sea lion population and fisheries information. Success of management scenarios is determined against two criteria, both of which involve keeping the sea lion population at or above 90 % of a modelled carrying capacity (6,987 mature individuals). Due to a lack of information on the pre-sealing abundance of the New Zealand sea lion, it is unclear whether the modelled carrying capacity represents a cap on sea lion recovery. Here, I use published estimates of genetic diversity based on microsatellite loci (expected heterozygosity, H
e) of the New Zealand sea lion and other otariid species to estimate historical effective population size (N
e). I then use existing knowledge of the ratio of N
e to census population size (N
C) to determine a historical census population size of these species. Genetical estimates of historical N
e suggest that NZ sea lions were considerably more abundant (>68,000 individuals) historically than the current population estimate (11,855 animals). Importantly, the genetical estimate of historical population size suggests that the modelled carrying capacity (6,987 mature sea lions) is likely an underestimation of recovery potential of the species; hence, current management maybe limiting the recovery of the species.
In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P-values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this article we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology, and psychology. We emphasize the following points:
New Zealand moa (Aves: Dinornithiformes) are the only late Quaternary megafauna whose extinction was clearly caused by humans. New Zealand offers the best opportunity to estimate the number of people involved in a megafaunal extinction event because, uniquely, both the Polynesian settlement of New Zealand and moa extinction are recent enough to be dated with a high degree of precision. In addition, the founding human population can be estimated from genetic evidence. Here we show that the Polynesian population of New Zealand would not have exceeded 2,000 individuals before extinction of moa populations in the habitable areas of the eastern South Island. During a brief (<150 years) period and at population densities that never exceeded ~0.01 km−2, Polynesians exterminated viable populations of moa by hunting and removal of habitat. High human population densities are not required in models of megafaunal extinction.
We describe an extinct parrot from late Quaternary fossil bone deposits on the Chatham Islands, located c. 800 km east of mainland New Zealand. Mitochondrial DNA analyses and osteological characters confirm that the Chatham Islands parrot was a sister taxon to the New Zealand kaka (Nestor meridionalis Gmelin, 1788). The relatively large femur : humerus length ratio and broad pelvis of the Chatham Islands parrot indicate that it had a more terrestrial habit than the kaka. Stable dietary isotope analyses (δ 15N and δ 13C) of Chatham Islands parrot bones suggest that the species may have been mainly herbivorous, although further analyses are required to confirm this. The presence of Chatham Islands parrot bones in early midden deposits shows that the species persisted into the post-settlement era, and became extinct possibly as a result of habitat loss, hunting pressure, and rat predation following initial Polynesian settlement of the islands (sometime between the 13th and 16th centuries AD).
Concentrations of total mercury ([THg]) and selenium ([TSe]) were measured in several tissue compartments in Steller sea lion (Eumetopias jubatus) pups; in addition we determined specific compartment and body burdens of THg. Compartmental and body burdens were calculated by multiplying specific compartment fresh weight by the [THg] (summing compartment burdens equals body burden). In all 6 pup tissue sets (1) highest [THg] was in hair, (2) lowest [THg] was in bone, and (3) pelt, muscle and liver burdens contributed the top three highest percentages of THg body burden. In 5 of 6 pups the Se:Hg molar ratios among compartments ranged from 0.9 to 43.0. The pup with the highest hair [THg] had Se:Hg molar ratios in 9 of 14 compartments that were ⩽0.7 potentially indicating an inadequate [TSe] relative to [THg].
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.
Holocene New Zealand sea lion (Phocarctos hookeri) bones collected from the north of New
Zealand’s South Island strengthen existing evidence for the former Holocene presence of
breeding colonies of P. hookeri on mainland New Zealand. The taxonomic identity of Phocarctos
bones is confirmed using both morphology and ancient DNA analysis. Five radiocarbon dates
on four adult and one pup bone from Creighton’s Cave near Paturau, northwest Nelson, ranged
from 1290930 yr BP to 5430930 yr BP. Three radiocarbon dates on pup bones spanning 200
14C yr (1550930 yr BP to 1390930 yr BP) reveal that a prehistoric breeding rookery was present
at Delaware Bay, Nelson, until shortly before the time of human arrival c. AD 1280 (670 yr BP).
The Delaware Bay site in particular provides a valuable ‘snapshot’ of coastal New Zealand
faunas shortly before human arrival, one that has potential to enhance our understanding of
changes in the endemic coastal fauna associated with human colonisation.
A New Zealand example illustrates the potential of foraging efficiency (FE) measures to inform not only on human–prey dynamics, but also to help identify situations where mobility is constrained or stimulated. Marked declines in Māori molluscan FE, coupled with increased shellfish usage, are identified over a ca. 450-year period at the coastal locality of Harataonga Beach, New Zealand. The potential effects of climate change are considered using newly available southwest Pacific multi-proxy records and temperature sensitive species, but correlations are lacking. The molluscan results signal possible restrictions on logistic and/or residential mobility in late prehistory, while evidence from the broader cultural landscape points to increasing agricultural investments and marked social competition. The Ideal Free Distribution model (IFD) is used to consider regional-scale interactions between foraging efficiency, agricultural developments, and competition, and their effects on mobility. Geographic and temporal variation in the patterning and causes of population movements is highlighted through this model, particularly differences between large game foragers in the south and populations with mixed economies in the north. In late prehistory, many northern areas including Harataonga apparently experienced reductions in the geographic scale of population movements, coupled with intensified intra-territorial mobility. The latter was an outcome of labour being widely dispatched across tribal territories, quasi-specialisation in subsistence tasks, and pooling and exchange of resources through a variety of social mechanisms which often involved population movements.
Four depositional episodes based on sand deposits and the soils on them are proposed for Holocene coastal sand dunes on Chatham Island: Te Onean Depositional Episode (c. 5,000 to 2,200 years BP), Okawan Depositional Episode (c. 2,200 to 450 years BP), Kekerionean Depositional Episode (c. 450 to 150 years BP) and Waitangian Depositional Episode (c. 150 years BP to present day). Each depositional episode has two phases: an unstable phase with a high rate of deposition and no soil formation, followed by a stable phase with a low rate of deposition and soil formation. The Okawan, Kekerionean, and Waitangian episodes closely match late Holocene depositional episodes on the New Zealand mainland. The earliest human occupation remains (Moriori) are in Kekerionean sands and the inferred date for Moriori settlement of Chatham Island is between 400 and 450 years BP. Bones of Hooker's sea lion are found in Te Onean and Okawan deposits. The most recent bones are in Kekerionean middens and it is inferred that Hooker's sea lion was driven from the Chatham Islands by human predation. The depositional episodes appear to be unrelated to sea level changes, tectonic activity, or cultural influence. It is suggested that they may be related to coastal erosion initiated by storms.
Tipping points - where systems shift radically and potentially irreversibly into a different state - have received considerable attention in ecology. Although there is convincing evidence that human drivers can cause regime shifts at local and regional scales, the increasingly invoked concept of planetary scale tipping points in the terrestrial biosphere remains unconfirmed. By evaluating potential mechanisms and drivers, we conclude that spatial heterogeneity in drivers and responses, and lack of strong continental interconnectivity, probably induce relatively smooth changes at the global scale, without an expectation of marked tipping patterns. This implies that identifying critical points along global continua of drivers might be unfeasible and that characterizing global biotic change with single aggregates is inapt.
1. Heterochronous data have been used to study demographic changes in epidemiology and ancient DNA studies, revolutionizing our understanding of complex evolutionary processes such as invasions, migrations and responses to drugs or climate change. While there are sophisticated applications based on Markov-Chain Monte Carlo or Approximate Bayesian Computation to study these processes through time, summarizing the raw genetic data in an intuitively meaningful graphic can be challenging, most notably if identical haplotypes are present at different points in time.
2. We present temporal networks, an attractive way to display and summarize relationships within the heterochronous data so commonly used in ancient DNA or epidemiological research. TempNet is a user-friendly R script that creates journal-quality figures from genetic data in standard formats (FASTA, CLUSTAL, etc.). These figures are customizable and interactive within the R graphics window. Using three examples, we demonstrate that TempNet can deal with standard-sized datasets, as well as datasets of hundreds of sequences from fast-evolving organisms.
3. Temporal networks are flexible ways to illustrate genetic relationships through time. Furthermore, this approach is not limited to time-stamped data, but can also be used for different data partitioning strategies, such as spatial or phenotypic groupings. The R script presented here will be useful in illustrating complex genetic relationships between groups.
The last 6000 years are of particular interest to the understanding of the Earth System because the boundary conditions of the climate system did not change dramatically (in comparison to larger glacial–interglacial changes), and because abundant, detailed regional palaeoclimatic proxy records cover this period. We use selected proxy-based reconstructions of different climate variables, together with state-of-the-art time series of natural forcings (orbital variations, solar activity variations, large tropical volcanic eruptions, land cover and greenhouse gases), underpinned by results from General Circulation Models (GCMs) and Earth System Models of Intermediate Complexity (EMICs), to establish a comprehensive explanatory framework for climate changes from the Mid-Holocene (MH) to pre-industrial time. The redistribution of solar energy, due to orbital forcing on a millennial timescale, was the cause of a progressive southward shift of the Northern Hemisphere (NH) summer position of the Intertropical Convergence Zone (ITCZ). This was accompanied by a pronounced weakening of the monsoon systems in Africa and Asia and increasing dryness and desertification on both continents. The associated summertime cooling of the NH, combined with changing temperature gradients in the world oceans, likely led to an increasing amplitude of the El Niño Southern Oscillation (ENSO) and, possibly, increasingly negative North Atlantic Oscillation (NAO) indices up to the beginning of the last millennium. On decadal to multi-century timescales, a worldwide coincidence between solar irradiance minima, tropical volcanic eruptions and decadal to multi-century scale cooling events was not found. However, reconstructions show that widespread decadal to multi-century scale cooling events, accompanied by advances of mountain glaciers, occurred in the NH (e.g., in Scandinavia and the European Alps). This occurred namely during the Little Ice Age (LIA) between AD ∼1350 and 1850, when the lower summer insolation in the NH, due to orbital forcing, coincided with solar activity minima and several strong tropical volcanic eruptions. The role of orbital forcing in the NH cooling, the southward ITCZ shift and the desertification of the Sahara are supported by numerous model simulations. Other simulations have suggested that the fingerprint of solar activity variations should be strongest in the tropics, but there is also evidence that changes in the ocean heat transport took place during the LIA at high northern latitudes, with possible additional implications for climates of the Southern Hemisphere (SH).
We investigate a neutral model for speciation and extinction, the constant rate birth–death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees—i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.