Catherine J. Collins

Asymmetric dispersal of southern bull-kelp (Durvillaea antarctica) adults in coastal New Zealand: testing an oceanographic hypothesis

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.

Extinction and recolonization of coastal megafauna following human arrival in New Zealand

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 worlds 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.

Pre-human New Zealand sea lion (Phocarctos hookeri) rookeries on mainland New Zealand

Holocene New Zealand sea lion (Phocarctos hookeri) bones collected from the north of New Zealands 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 Creightons Cave near Paturau, northwest Nelson, ranged from 1290±30 yr BP to 5430±30 yr BP. Three radiocarbon dates on pup bones spanning 200 14C yr (1550±30 yr BP to 1390±30 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.

Evidence of a Native Northwest Atlantic COI Haplotype Clade in the Cryptogenic Colonial Ascidian Botryllus schlosseri.

The colonial ascidian Botryllus schlosseri should be considered cryptogenic (i.e., not definitively classified as either native or introduced) in the Northwest Atlantic. Although all the evidence is quite circumstantial, over the last 15 years most research groups have accepted the scenario of human-mediated dispersal and classified B. schlosseri as introduced; others have continued to consider it native or cryptogenic. We address the invasion status of this species by adding 174 sequences to the growing worldwide database for the mitochondrial gene cytochrome c oxidase subunit I (COI) and analyzing 1077 sequences to compare genetic diversity of one clade of haplotypes in the Northwest Atlantic with two hypothesized source regions (the Northeast Atlantic and Mediterranean). Our results lead us to reject the prevailing view of the directionality of transport across the Atlantic. We argue that the genetic diversity patterns at COI are far more consistent with the existence of at least one haplotype clade in the Northwest Atlantic (and possibly a second) that substantially pre-dates human colonization from Europe, with this native North American clade subsequently introduced to three sites in Northeast Atlantic and Mediterranean waters. However, we agree with past researchers that some sites in the Northwest Atlantic have more recently been invaded by alien haplotypes, so that some populations are currently composed of a mixture of native and invader haplotypes.

Strong Phylogeographic Structure in a Sedentary Seabird, the Stewart Island Shag (Leucocarbo chalconotus)

New Zealands 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.

Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations.

While terrestrial megafaunal extinctions have been well characterized 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 Zealands 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 overhunting, 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.

Historical population size of the threatened New Zealand sea lion Phocarctos hookeri

Marine mammal species were exploited worldwide during periods of commercial sealing in the 18th and 19th centuries. For many of these species, an estimate of the pre-exploitation abundance of the species is lacking, as historical catch records are generally scarce and inaccurate. Genetic estimates of long-term effective population size provide a means to estimate the pre-exploitation abundance. Here, we apply genetic methods to estimate the long-term effective population size of the subantarctic lineage of the New Zealand sea lion (NZ sea lion), Phocarctos hookeri. This species is predominantly restricted to the subantarctic islands, south of mainland New Zealand, following commercial sealing in the 19th century. Today, the population consists of ∼9,880 animals and population growth is slow. Auckland Island breeding colonies of NZ sea lion are currently impacted by commercial trawl fisheries via regular sea lion deaths as bycatch. In order to estimate sustainable levels of bycatch, an estimate of the populations carrying capacity (K) is required. We apply the genetically estimated long-term effective population size of NZ sea lions as a proxy for the estimated historical carrying capacity of the subantarctic population. The historical abundance of subantarctic NZ sea lions was significantly higher than the target values of K employed by the contemporary management. The current management strategy may allow unsustainable bycatch levels, thereby limiting the recovery of the NZ sea lion population toward historical carrying capacity.

The Pacific Rat Race to Easter Island: Tracking the Prehistoric Dispersal of Rattus exulans Using Ancient Mitochondrial Genomes

The location of the immediate eastern Polynesian origin for the settlement of Easter Island (Rapa Nui), remains unclear with conflicting archaeological and linguistic evidence. Previous genetic commensal research using the Pacific rat, Rattus exulans; a species transported by humans across Remote Oceania and throughout the Polynesian Triangle, has identified broad interaction spheres across the region. However, there has been limited success in distinguishing finer-scale movements between Remote Oceanic islands as the same mitochondrial control region haplotype has been identified in the majority of ancient rat specimens. To improve molecular resolution and identify a pattern of prehistoric dispersal to Easter Island, we sequenced complete mitochondrial genomes from ancient Pacific rat specimens obtained from early archaeological contexts across West and East Polynesia. Ancient Polynesian rat haplotypes are closely related and reflect the widely supported scenario of a central East Polynesian homeland region from which eastern expansion occurred. An Easter Island and Tubuai (Austral Islands) grouping of related haplotypes suggests that both islands were established by the same colonization wave, proposed to have originated in the central homeland region before dispersing through the south-eastern corridor of East Polynesia.

Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility

The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700–400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society.