Shallow but striking genetic structure in the highly connected New Zealand sand dollar (Fellaster zelandiae)
Ian S. Dixon-Anderson
A
Abstract
Phylogeographic patterns can reveal the physical environmental processes that shape biodiversity. Marine species often have dispersive larval stages, but might not be well-connected over large distances. Sand dollars, for example, often show regional isolation but local connectivity.
This study sought to quantify the population genomic structure of the New Zealand sand dollar, Fellaster zelandiae.
Sequencing of the cytochrome c oxidase I (COI) gene fragment determined the phylogenetic relationship of Fellaster with other sand dollars globally, and genotyping-by-sequencing (40,725 single-nucleotide polymorphisms) revealed the phylogeography of this species around New Zealand.
The genus Fellaster was resolved as sister to its Australian counterpart, Arachnoides. Fellaster zelandiae showed evidence of strong connectivity among populations.
Small-scale genetic variation between northern and southern populations appears to be consistent with biogeographic patterns seen in other coastal species in New Zealand and is probably driven by isolation of some regions by oceanographic features incluing the East Auckland Current, East Cape Current and Southland Current.
While the strong connectivity of many contemporary Fellaster zelandiae populations is likely to be the result of a long-lived larval stage, gene flow may reduce in the future if larval development times decrease.
Keywords: biogeography, Clypeasteroida, echinoderms, GBS, genotyping-by-sequencing, marine invertebrate, phylogeny, population genetics, sand dollar.
Introduction
Marine biogeography
Phylogeographic structure in marine species can shed light on how physical environmental processes shape biodiversity (Emerson and Hewitt 2005; Beheregaray 2008; Kumar and Kumar 2018), which is of particular importance as species distributions shift in response to global warming (Banks et al. 2010; Lo Brutto et al. 2011; Halbritter et al. 2015). While traditional genetic approaches, such as sequencing one or a few markers, have helped us understand broad-scale patterns of marine biogeography (e.g. Palumbi 1996), newer, high-resolution genomic tools can provide powerful and detailed insights into cryptic diversity, timelines of species divergence, migration, and dispersal abilities (Rocha et al. 2013; Fraser et al. 2016; Vaux et al. 2023).
Global analyses of marine biogeography have found distinct endemicity of marine biota in 30 different realms (Briggs 1995), with ~40% of species being unique to each realm (Costello et al. 2017). New Zealand has been identified as one such unique biogeographic realm, with the large ocean basins acting to separate many New Zealand species from other regions. Towards the end of the Oligocene (c. 23 Ma), the Zealandia plate was thought to be partially ‘drowned’ (Waters and Craw 2006; Knapp et al. 2007), which is suggested to have reset many New Zealand ecosystems (Knapp et al. 2007; Gordon et al. 2010). Trans-Tasman dispersal and resettlement from Australia has been inferred from genetic data to occur in some species whose larval stages can last 5 months or more (Ovenden et al. 1992; Chiswell et al. 2003; Waters et al. 2007; Thomas et al. 2021); however, trans-Tasman dispersal for shorter larval stage organisms are less likely to succeed (Ross et al. 2009). The resulting unique biota and considerable isolation of New Zealand makes it an intriguing location for biogeographic research.
New Zealand marine hydrological processes and geographic patterns are particularly influenced by the Cook Strait (Chiswell et al. 2021), separating the North and South Islands, with fast tidal flows and deep bathymetry causing biogeographic disjunctions on the upper South Island in several shallow water marine taxa (Goldstien et al. 2006). This oceanographic separation is relatively new on geological timescales, with the estimated final formation of the Cook Strait being c. 500,000 years ago (Trewick and Bland 2012). A land bridge connected the two islands both prior to the Strait formation (Alloway et al. 2007) and during Pleistocene sea regressions, including during the last glacial period c. 20,000 years ago. This transient isolation caused differentiation of population structures in Hector’s and Maui dolphins (Alvarez-Costes et al. 2025), and so the Cook Strait area may be the epicentre of both north–south and east–west genetic breaks. This central location may also have the most genetic mixing from recent recolonisation efforts of these different populations.
Further south, the Chatham Rise off the eastern coast of the South Island’s Banks Peninsula forces a convergence of currents and pushes the Southland Current offshore (Nodder et al. 2003; Sutton 2003; Hopkins et al. 2010). Shorter larval development windows of species such as the mollusc Lunella smaragda, and brachiopods Terebratella sanguinea and Liothyrella neozelancia can result in genetic isolation between stretches of coast in New Zealand (Ostrow 2004; Chiswell and Booth 2008; Arranz et al. 2021), whereas species with longer larval stages such as the crustacean Jasus edwardsii, the sea urchin Centrostephanus rodgersii, and molluscs Scutus breviculus and Austrolittorina antipodum show an absence of population subdivision across New Zealand (Ovenden et al. 1992; Waters et al. 2007; Thomas et al. 2021). These differences raise questions about how ubiquitous the influences of abiotic and ecological forces are versus hydrological and geographic factors in shaping biodiversity in New Zealand.
Fellaster zelandiae population dynamics
Fellaster zelandiae (Gray, 1885) (‘kina papa’ in te Reo Māori) is an irregular echinoid (Clypeasteroida) that acts as a benthic–pelagic coupler and bioturbator, and is endemic to Aotearoa (New Zealand). Fellaster zelandiae is the only extant species in its genus, and has populations distributed around New Zealand. Classical taxonomic study has determined that F. zelandiae populations around New Zealand belong to a single species with no notable morphological differences (Durham 1955). Fellaster zelandiae are broadcast spawners whose planktotrophic larval stages develop for several weeks in the water column until they metamorphose into juveniles. For such species, larval dispersal time is an important factor in the distribution and genetic connectivity of populations between geographically distinct regions (Strathmann 1978). Generally, the longer a larva spends in the pelagic period, the greater is the potential connectivity of populations (Strathmann 1974; Shanks 2009). In many echinoids, the length of the larval period is strongly influenced by water temperature (Bosch et al. 1987; Hoegh-Guldberg and Pearse 1995).
Fellaster zelandiae has a larval development period of 28 days or more (Bunckenburg 2003), which is longer than other sand dollar species that range from 5 to 15 days, and rarely last more than 3 weeks (Caldwell 1972; Emlet 1986a; Chen and Chen 1993). We hypothesise that the prolonged time spent in the water column give F. zelandiae a greater chance to disperse compared to other sand dollar species, and could enhance gene flow among populations. Although other genetic studies of regular and irregular echinoderms have shown cryptic speciation (Coppard et al. 2013; Bronstein et al. 2017), or considerable phylogeographic structure (Lessios et al. 1999; Coppard and Lessios 2017), no previous genetic work has been undertaken on F. zelandiae. Determining the extent of genetic connectivity in F. zelandiae will help improve our understanding of the processes driving biogeographic patterns in marine species with medium-to-long larval periods. As Fellaster zelandiae occurs throughout coastal New Zealand from 35 to 46°S, and across diverse environmental gradients (hydrology, primary productivity, temperature and pH), genetic research could also provide insights into any local adaptation and phenotypic plasticity.
Aims
All previous ecological work has assumed the uniformity of Fellaster zelandiae populations without considering spatial patterns in phenotypic plasticity or genetic diversity (Bunckenburg 2003; Grkovic and Copp 2013; Karelitz et al. 2017). Here, we set out to test the following questions: (1) where does Fellaster zelandiae sit phylogenetically among Clypeasteroida; (2) how homogeneous is the genetic structure of Fellaster zelandiae across its geographic range; and (3) do classical population breaks seen in coastal taxa apply to Fellaster zelandiae? We tested these questions by genetic analysis of 15 populations encompassing the biogeographic range of Fellaster zelandiae.
Materials and methods
Field sampling
Nine geographic regions were identified by hydrological and geographical features around New Zealand (Fig. 1a) on the basis of previous work to model larval connectivity (Chiswell and Rickard 2011). Fifteen locations of interest with potential populations of Fellaster zelandiae were identified across New Zealand on the basis of recorded observations. Intact living adult sand dollars were collected by free-diving at nine subtidal sites, by hand from four intertidal sandy environments, and by dredge at two benthic sites (Fig. 1b). Sampling in Regions 1, 2, 5, 7 and 9 was successful, with live individuals collected from at least two distinct locations for each region. In Regions 3, 4 and 8, only one site was successfully sampled, with failed sampling attempts across more of each region due to poor sea conditions. At Region 6, we found evidence of populations (broken tests washed up onshore) but were unable to collect fresh samples.
(a) New Zealand currents: Tasman Front (TF), North Cape Eddy (NCE), East Auckland Current (EAUC), West Auckland Current (WAUC), East Cape Eddy (ECE), D’Urville Current (DC), East Cape Current (ECC), Wairarapa Eddy (WE), Westland Current (WC), Southland Current (SC), Antarctic Circumpolar Current (ACC) and Subantarctic Front (SAF). New Zealand water masses: subtropical water (pink), subtropical front (purple), coastal water (green), Southland front (yellow) and subantarctic water (blue). (b) Distribution of genetic samples taken of Fellaster zelandiae with nine geographic regions of interest, and locations of interest. Successful sequencing of >10 samples (purple), 6–10 samples (orange) or 1–5 samples (red).

At each site, more than the requisite number of individuals was collected initially (i.e. 70), and 27 healthy-looking individuals were selected from the pool (Nazareno et al. 2017). Suitability was judged on the basis of symmetry, a lack of predation marks and full spine coverage of the tests. Unhealthy individuals and surplus healthy individuals were returned to their beds. Collected samples were preserved immediately in 95% EtOH, and then stored at −80°C within a few days of collection. Tissue samples were taken for genetic analysis by opening the oral surface and removing 3 g of soft tissue from the intestinal and gonadal area.
DNA extraction and QC
Tissue was subsampled and rinsed three times with ultrapure H2O to remove ethanol. DNA was extracted using a Qiagen DNeasy 96 Blood and Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol, yielding ~20 μL of DNA of varying concentrations per sample. DNA was used in both of the following procedures.
COI
Partial sequencing of the cytochrome c oxidase I (COI) gene fragment was conducted on representative subsamples from several regions around New Zealand, by polymerase chain reaction (PCR), by using the modified Leray primers EchinoF1 5′-TTT CAA CTA ATC ATA AGG ACA TTG G-3′ (Ward et al. 2008; Lee et al. 2019) and HCO 5′ – TAA ACT TCA GGG TGA CCA AAA AAT CA – 3′ (Folmer et al. 1994; Leray et al. 2013), hereafter called forward and reverse primers. Each PCR reaction included 12.5 μL of MyTaq Red Mix (Bioline Reagents, Meridian Bioscience, London, UK), 1 μL of forward primer (10 μM), 1 μL of reverse primer (10 μM), and 8.5 μL of ultra-pure H2O (Invitrogen, Thermo-Fischer Scientific, Carlsbad, CA, USA), along with 2 μL of extracted sample DNA. Negative PCR controls were included, along with positive controls by using a seastar Odontaster validus template. A PCR cycle was run using a start cycle of 94°C for 2 min, followed by 35 cycles of 94°C for 30 s, 50°C for 30 s and 72°C for 1 min, and then a final elongation step (72°C, 10 min). PCR products were purified using MEGA quick-spin plus Fragment DNA purification kit (iNtRON Biotechnology, Gyeonggi, South Korea), and sequenced by the Genetic Analysis Services at the University of Otago, New Zealand (see https://gas.otago.ac.nz/services), by using the forward primer, on an ABI 3730xl DNA Analyser.
COI sequences of six Fellaster zelandiae specimens (GenBank Accession number PX096134-PX096139, this study) from Regions 1, 2, 8 and 9 were generated, and visually checked for quality, editing ambiguous base calls where appropriate, in Geneious Prime software (ver. 2025.0.3, see https://www.geneious.com; Kearse et al. 2012). COI sequences of 35 other species of sand dollar (superorder: Luminacea) were retrieved from NCBI GenBank from prior studies (Coppard et al. 2013; Coppard and Lessios 2017; Endo et al. 2018; Lee et al. 2023). All COI sequences were aligned using Clustal Omega (ver. 1.2.2, see https://www.ebi.ac.uk/jdispatcher/msa/clustalo?stype=protein; Sievers et al. 2011; Katoh 2021; Sievers and Higgins 2021) in the Geneious Prime software by using default parameters. The final trimmed alignments consisted of 40 sequences of 618 bp DNA in the COI gene. Smart Model Selection software (see http://www.atgc-montpellier.fr/sms/; Lefort et al. 2017) in PhyML (ver. 3.0, see http://www.atgc-montpellier.fr/phyml/; Guindon et al. 2010) was used to select the optimal model by using likelihood-based criteria of Bayesian information criterion (BIC). The model choice (HKY85 + G + I) was run in Geneious Prime software to assess the strength of the phylogenetic relationship of each node by bootstrapping (Felsenstein 1985), by using 50,000 permutations. We additionally ran a Bayesian inference Markov-chain Monte Carlo (MCMC) analysis by using MrBayes (ver. 3.2, see https://github.com/NBISweden/MrBayes/; Ronquist et al. 2012). A HKY model with gamma-distributed rates was performed using the following parameters: ngen = 1,000,000, samplefreq = 100, nchains = 4, savebrlens = yes, printfreq = 1000, diagnfreq = 5000, burninfrac = 0.25. A consensus tree with posterior probabilities (PP) was visualised.
Divergence times (T) were calculated from Fellaster zelandiae to sister species by using the following equation:
where proportion of genetic divergence (D) was measured from averaged substitutions per site between two lineages, and the rate of sequence evolution (μ) was estimated at 2% per million years for COI sequences to consider both the conservative classical estimates of echinoderms at 1–2% (Bermingham and Lessios 1993; Lessios 2008) and the newer estimates of arctic echinoderms of 4–6% (Foltz et al. 2008; Loeza-Quintana et al. 2019).
Genotyping by sequencing (GBS)
Extracted DNA was cleaned using MEGA quick-spin plus Fragment DNA purification kit (iNtRON Biotechnology, Gyeonggi, South Korea) to remove degraded DNA fragments. RNAse A (Sigma–Aldrich, Burlington, MA, USA) was added into cleaned solutions to remove RNA contamination.
The GBS library of 166 samples was constructed according to the methods outlined in Elshire et al. (2011), with modifications as outlined in Dodds et al. (2015). One pooled GBS library was prepared using an ApeKI restriction enzyme digest and included a negative control sample (no DNA) for each plate of 96 at AgReseach Invermay Agricultural Centre (Mosgiel, New Zealand). Libraries underwent a Pippin Prep (SAGE Science, Beverly, MA, USA) to select fragments in the size range of 220–340 bp. Single-end sequencing (1 × 101 bp) was performed on a NovaSeq6000 (Illumina Inc., San Diego, CA, USA) by using v1.5 chemistry to achieve ~22 gigabases of data. Raw fastq files were quality checked (QC) using a custom QC pipeline (DECONVQC, see https://github.com/AgResearch/DECONVQC; Dodds et al. 2015). As one of the QC steps, raw fastq files were quality checked using FastQC (ver. 0.10.1, see http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). ExAmp duplicates were removed using Clumpify (see https://github.com/BioInfoTools/BBMap/blob/master/sh/clumpify.sh) with a dupe distance setting of 15,000. Demultiplexing and sequence clean-up were undertaken using UNEAK Tassel (ver. 3.0.173, see https://www.maizegenetics.net/tassel; Lu et al. 2013). Raw reads were processed as input fastq data and a key file supplying the barcodes through this reference-free single-nucleotide polymorphism (SNP) detection pipeline.
As no reference genome was available as a scaffold, sequences were assembled de novo (BioSample accession numbers SAMN50484970–SAMN50485130). Allelic depth values were processed through a kinship by using GBS with Depth adjustment (KGD, ver. 1.2.2, see https://github.com/AgResearch/KGD) method (Dodds et al. 2015). Allelic depth values were corrected for ExAmp duplication by applying the beta-binomial model. Parameter settings used are available in ‘run_kgd.R’. Samples with a maximum depth of 1 or mean depth <0.01 were removed. SNPs with a MAF of 0 or depth of <0.01 were removed. A Hardy–Weinberg disequilibrium >0.05 was applied as an additional filter.
The remaining analyses were performed in R (ver. 4.4.2, R Foundation for Statistical Computing, Vienna, Austria, see https://www.r-project.org/), following previous methodologies from the laboratory (Padovan et al. 2020; Vaux et al. 2023). Packages used include adegenet (ver. 2.1.10, see https://CRAN.R-project.org/package=adegenet; Jombart 2008), vcfR (ver. 1.15.0, see http://cran.r-project.org/package=vcfR; Knaus and Grünwald 2017), ggplot2 (ver. 3.5.1, see https://CRAN.R-project.org/package=ggplot2; Wickham 2016), VariantAnnotation (ver. 1.52.0, see https://github.com/Bioconductor/VariantAnnotation; Obenchain et al. 2014), poppr (ver. 2.9.6, see https://CRAN.R-project.org/package=poppr; Kamvar et al. 2015, 2014), devtools (ver. 2.4.5, H. Wickham et al., see https://CRAN.R-project.org/package=devtools), SeqVarTools (ver. 1.46.0, S. M. Gogarten and X. Zheng, see https://github.com/smgogarten/SeqVarTools), pophelper (ver. 2.3.1, see https://github.com/royfrancis/pophelper; Francis 2017), vegan (ver. 2.6-10, J. Oksanen et al., see https://CRAN.R-project.org/package=vegan/), SNPRelate (ver. 1.40.0, see https://github.com/zhengxwen/SNPRelate; Zheng et al. 2012), LEA (ver. 3.18.0, E. Frichot, O. Francois and C. Gain, see https://bioconductor.org/packages/release/bioc/html/LEA.html; Frichot and François 2015) and BiocManager (ver. 1.30.25, M. Morgan and M. Ramos, see https://cran.r-project.org/package=BiocManager). Scripts are available in the Supplementary material (Files S1–S4).
A latent-factor model for ecological and evolutionary genomic associations program (LEA) was run in R by using sparse non-negative matrix factorisation (snmf) to determine ancestry coefficients of individuals from different clusters and the partitioned genetic variation in cluster assignments. The model was run using high variation conditions with high repetitions to determine the best fit (K = 1:10, repetitions = 50, entropy = T). Cluster numbers were plotted against cross-entropy alpha values to investigate likely population splits and common ancestry. The ancestry coefficients for all genetic samples were plotted on admixture plots sorted by beach and region for all K. Expected heterozygosity (HE) and observed heterozygosity (HO) were calculated (Supplementary Table S1). Pairwise fixation index values (FST) were calculated (Supplementary Table S2).
A principal component analysis (PCA) was performed and the primary and secondary components were plotted to visualise the location differences. A plot matrix of the first four principal components was generated to visualise the interactive effects of each pair of PCs on the differences. Graphs of the first and second PCs were compared to visually distinct genetic clusters across admixture plots and mapped across geographical and hydrological features to identify population breaks for K = 2, 3 and 4.
Results
COI data
Smart Model Selection in PhyML found that the best substitution model was HKY85+G+I (Hasegawa et al. 1985), with an estimated 0.593 proportion of invariable sites, four substitution-rate categories, and an estimated 0.919 gamma shape parameter. A consensus tree was built from 40 COI sequences: 34 sequences of 34 known species of sand dollar and 6 sequences of Fellaster zelandiae from 6 different populations (Fig. 2). Clades were resolved similarly to previous literature (Lee et al. 2023) on the basis of bootstrap values (BV) and posterior probabilities (PP). Fellaster zelandiae was resolved as a sister genus to the genus Arachnoides (BV = 83, PP = 1.00), and then to three species of the genus Clypeaster (BV = 99, PP = 0.78). Percentage relatedness (Table S3) of base reads showed the same genus relationship, with Fellaster relatedness to Arachnoides being the greatest (85.8–86.6%), followed by the relatedness to Clypeaster (81.5–84.5%). The relatedness of all other genera to F. zelandiae ranged from 79.5 to 82.8%. These results were supported by the Bayesian inference MCMC analysis run using MrBayes, which provided strong posterior probability support for the sister relationships (0.99–1.00). Divergence times of Fellaster to Arachnoides genera were calculated as 3.3–3.6 Ma (Table S4), with divergence between Fellaster and all other species being 3.9–4.4 Ma. The next-closest relatives to Fellaster zelandiae were Clypeaster virescens (16.4% different) and Clypeaster japonica (15.6% difference), helping confirm that the genus Fellaster sits within the family Clypeasteridae.
Phylogenetic relationship of 33 species of sand dollars (Echinodermata: Irregularia) from 618-bp COI sequences. Nodal supports are shown as bootstrap values (BV) as a percentage (above) and posterior probabilities (PP) from 0 to 1 (below). BV below 70% and PP below 0.7 are not shown.

Analysis of COI sequencing data found little evidence of speciation or major genetic divergences among the populations of Fellaster zelandiae, because the p-distance of the Tauranga site was 0.045 and p-distances of the five other F. zelandiae populations were 0.012–0.032 (Table S5). The values of percentage relatedness of the six F. zelandiae specimens were all >99%, indicating no evidence of cryptic speciation. All but one sample of F. zelandiae shared near-identical COI haplotypes: Ahipara, New Plymouth and Te Waewae Bay shared identical haplotypes (from Regions 1, 1, and 9 respectively), the Timaru sample (Region 8) had one G–A substitution, and the sample from Hikuwai (Region 2) had a single G–A substitution in a different region. Only the sample from Tauranga was distinct, with five substitutions along the sequence (A–G, C–T, G–A, G–A, T–C) different from all other samples, including the Hikuwai sample in the same region.
GBS
In total, 40,903 SNPs were detected with UNEAK for 166 Fellaster zelandiae from across the entire range of New Zealand, with a mean sample depth of 2.7 (Supplementary Fig. S1). The Standard Hardy–Weinberg filter removed 178 SNPs (Supplementary Fig. S2) for a total of 40,725 SNPs used for analyses. The MAF distribution was skewed to the left, indicating good diversity of the samples (Supplementary Fig. S3). FST values were extremely low (greatest value = 0.025), indicating a very high genetic similarity (Supplementary Fig. S4, S5). Observed heterozygosity values were also very low (HO = 0.150) and less than expected values (HE = 0.222) indicating potential population substructure (Table S1).
Plots of the first four principal components (Supplementary Fig. S6) show no major population differences, but two subtle distinct clusters were differentiated by the first principal components (Fig. 3). Overall, population variation was low, with the first two principal components accounting for only 2 and 1% of variation. Cross-entropy values fitted to clusters (K) from LEA showed no appreciable decrease in value at any cluster greater than 1, indicating relative genetic homogeneity (Supplementary Fig. S7). Ancestry coefficients plotted as pie charts in geographic regions for K = 2, 3 and 4 indicated subtle breaks between north-eastern (Regions 2 and 3), north-western (Region 1), central (Regions 4 and 5) and southern (Regions 7, 8 and 9) regions (Fig. 4a, 5a, 6a). The distinction of the north-eastern population is the most prominent, occurring in each of the three assignment tests. Notation of the same groupings was made in a PCA plot to visualise the magnitude of the genetic difference (Fig. 4b, 5b, 6b). PCA clusters confirmed the distinction of the north-eastern population, while showing that the north-western and central distinctions were less prominent. Admixture clusters (K = 2, 3, 4) plotted by latitude were determined relevant in a subpopulation context to support the minor differences among geographic regions (Fig. 4c, 5c, 6c), because each additional cluster aligned with prominent geographical or hydrological features around New Zealand.
Site location and first two principal components from principal component analysis of 166 genetic sequences for Fellaster zelandiae colour-coded to location of the specimen.

Analysis of population genetics under an assumption of two subpopulations. (a) Population clusters of genetic samples plotted at each location, with distinctions between north-eastern (red) and southern (blue) subpopulations seen in the geographic breaks indicated by the dashed line. (b) Comparison of principal component analysis for Fellaster zelandiae, with differences between population groups highlighted in the coloured ovals of each population. (c) Subpopulation clustering (shading) compared to prominent hydrology (arrows), indicative of potential larval dispersal and discrete subpopulation. (d) Admixture plot with the clustering set to K = 2 for each of the 166 GBS sequences, resolving the population clusters of all samples by location.

Analysis of population genetics under an assumption of three subpopulations. (a) Population clusters of genetic samples plotted at each location, with distinctions among north-eastern (red), central (yellow) and southern (blue) subpopulations seen in the geographic breaks indicated by the dashed line. (b) Comparison of principal component analysis for Fellaster zelandiae, with differences among population groups highlighted in the coloured ovals of each population. (c) Subpopulation clustering (shading) compared to prominent hydrology (arrows), indicative of potential larval dispersal and discrete subpopulation. (d) Admixture plot with the clustering set to K = 3 for each of the 166 GBS sequences, resolving the population clusters of all samples by location.

Analysis of population genetics under an assumption of four subpopulations. (a) Population clusters of genetic samples plotted at each location, with distinctions among north-eastern (red), north-western (orange), central (yellow) and southern (blue) subpopulations seen in the geographic breaks indicated by the dashed line. (b) Comparison of principal component analysis for Fellaster zelandiae, with differences among population groups highlighted in the coloured ovals of each population. (c) Subpopulation clustering (shading) compared to prominent hydrology (arrows), indicative of potential larval dispersal and discrete subpopulation. (d) Admixture plot with the clustering set to K = 4 for each of the 166 GBS sequences, resolving the population clusters of all samples by location.

Discussion
These findings support the hypothesis that there is high gene flow in Fellaster zelandiae across New Zealand. However, the mechanisms that drive biogeographic breaks seen in many other New Zealand marine species may also have an influence on F. zelandiae population connectivity, predominantly seen in the subtle differences between northern and southern populations.
Phylogeny of Fellaster zelandiae
Our results place the genus Fellaster sister to the Australian genus Arachnoides, with an estimated divergence c. 3.4 Ma (Table S4) that vastly post-dates the formation of the deep ocean basin of the Tasman sea (Hayes and Ringis 1973; Weissel and Hayes 1977). Physical distance separating these two species coupled with both the need for long dispersal time for trans-Tasman transport (Chiswell et al. 2003) and the short larval window of Arachnoides placenta (Aung, 1975; Gonzalez-Bernat et al. 2013) suggests that these two species have become isolated and genetically distinct reasonably recently in geological timescales. An extinct south-eastern Australian species, Fellaster incisa, exists in the fossil record from the Pliocene (5.3–2.6 Ma) (Sadler and Pledge 1985; Holmes 1987). This species had a more southern distribution than the genus Arachnoides (Foster and Philip 1980) and it is possible that Fellaster incisa diverged from Arachnoides by geographical and ecological separation in Australia, and then dispersed to New Zealand by a chance dispersal event (e.g. by storms, zoochory or rafting on buoyant seaweed; Gillespie et al. 2012). The extinct Fellaster incisa may hence be ancestral to F. zelandiae, which was present in some Pliocene fossil records of New Zealand (Farquhar 1894). Recent trans-Tasman dispersal has also been inferred for another echinoderm found in New Zealand and Australia, Centrostephanus rodgersii (Thomas et al. 2021), although that species has much longer-lived echinopluteus transversus larvae thought to be for long-distance transport (Soars et al. 2009). Dispersal of Fellaster larvae remains a somewhat less plausible explanation for a past trans-Tasman dispersal event, given the shorter-lived larvae, and the length of time for passive particles to move across the Tasman Sea. For instance, 85% of satellite drifters released in Australia (Tasmania) arrived in New Zealand after 18 months (Cresswell 2000), indicating that the pace of movement in water currents is likely to be too slow for the development window of Fellaster, unless past currents were more rapid, or the pelagic larval period was longer.
Biogeography and connectivity of Fellaster zelandiae
Differentiation among populations of Fellaster zelandiae across New Zealand was low (Fig. 3), but the subtle structure between northern and southern populations suggests some level of reduced mixing, possibly driven by oceanography. Principal component analysis (Fig. 3) found that of these subpopulations, all specimens of the North Islands’ north-eastern and eastern coasts (Regions 2 and 3) were distinct from those in the rest of the country. Although other geographic differences emerged as the number of clusters increased, it is hard to definitively determine whether one cluster is more accurate than another. Rather, the display of greater cluster numbers can be thought of as a representation of minor allele differences, which may, over time, diverge. Presently, the genetic differences seen across all populations of F. zelandiae are remarkably low (Fig. 3, S4, Table S2), possibly owing to F. zelandiae being a species with a planktonic larval duration and dispersal that drives genetic homogeneity.
Two other echinoids in New Zealand, the sea urchin Evechinus chloroticus (‘kina’ in te Reo Māori) and Centrostephanus rodgersii, have also shown subtle genetic variation. However, only E. chloroticus’ dispersal across the entire country is useful for comparison, because the range of C. rodgersii is confined to the warmer waters (>15°C) in northern New Zealand (Pecorino et al. 2013). Original surveys using gel electrophoresis of five enzyme loci indicated that E. chloroticus had little or no variation among six populations (Mladenov et al. 1997), and the 4–6 week larval period was suggested to allow high gene flow (Barker 2013). However, subsequent analysis of microsatellite loci in the same species found restricted gene flow between the North and South Islands, as well as differences within and among fjords in Fiordland and between ecotypes of open coast and fjord populations (Perrin 2002). These differences were attributed to restricted larval dispersal in sheltered populations and to hydrology, as seen directly in Lamare (1998). The small differences seen in E. chloroticus used to infer subtle population differences may be taken into consideration here for F. zelandiae as these two species follow similar larval development patterns and timing.
When comparing the subtle difference seen in this study, Fellaster zelandiae populations from the north-west (Region 1) may connect to central (Regions 4 and 5), central may connect to the western coast (Region 6), the north-east (Region 2) may connect to the eastern coast (Region 3), and the south (Region 9) may connect to the south-east (Regions 7 and 8). However, unidirectional flow may prevent mixing of north-western (Region 1) and north-eastern (Region 2) groups, and geographic stretches of unsuitable substrate or habitat (gravel or mud and silt) in the fjords may be too large for larval dispersal and gene flow from central New Zealand (Region 5) and southern New Zealand (Region 9). The genetic separation of F. zelandiae on the eastern coast of the North Island (Regions 2 and 3) from other populations aligns with the prevailing East Auckland Current and East Cape Current (Fig. 4–6). The intensity and direction of these currents from north-west to east may reduce gene mixing with the north-west (Region 1). In all cluster analyses, the Chatham rise additionally acts as a barrier between north-eastern populations (Regions 2 and 3) and southern populations (Regions 7–9) as the Southland Current moves offshore at Banks Peninsula. Paired with poor sediment habitat of mud and gravel seen in the Kaikōura region, the north-eastern coast of the South Island may be a large geographic break between populations of F. zelandiae in the south and in the centre of the country. Our study is limited in determining the veracity of this idea because no DNA samples were able to be collected from the western coast of the South Island. Future work should look to gather genetic samples from this region to resolve such questions.
The strong connectivity in Fellaster zelandiae contrasts with the high phylogeographic structure observed in many New Zealand marine taxa, such as the green-lipped mussel, Perna canaliculus (Apte and Gardner 2002), three limpets of Cellana ornata, Cellana radians and Cellana flava (Goldstien 2005), two red algae of Agarophyton chilense and Agarophyton transtasmanicum (Huanel et al. 2020), and three species of whelks, namely, Buccinulum vittatum (Gemmell et al. 2018), Cominella maculosa (Dohner et al. 2018) and Cominella virgata (Walton et al. 2019). Many of these species have short to medium larval dispersal times of days to weeks, and have seen population structure form around the Cook Strait, between the west coast to east coast, from small geographic locations, and from environmental factors such as temperature (Waters and Roy 2004; Ross et al. 2009). Investigating F. zelandiae populations with clusters of K = 2–4 shows that these influences may be faintly present (Fig. 4–6), but the degree of difference is insufficient to quantify populations as distinct. The absence of much population subdivision in F. zelandiae across New Zealand aligns somewhat with species with very long larval dispersal duration, such as Jasus edwardsii (Ovenden et al. 1992), gastropod genera Scutus and Austrolittorina (Waters et al. 2007), and the sea star Patiriella regularis (Waters and Roy 2004; Ayers and Waters 2005). A similar geographic pattern has been seen in Patiriella regularis, where a low mean divergence of 0.96% between populations determined a north–south disjunction south of the Cook Strait (Ayers and Waters, 2005). These longer dispersal species often show little morphological variation, and genetic homogeneity.
The connectivity in Fellaster zelandiae contrasts with other echinoderm taxa, including the pantropical cidaroid sea urchin genus Eucidaris (Lessios et al. 1999), and with sand dollars: notably, the Atlantic genus Mellita (Coppard et al. 2013) the widespread genus Encope (Coppard and Lessios 2017), and the species Clypeaster subdepressus (Zigler et al. 2008). For the genera Mellita and Encope, phylogeographic analyses have found speciation along the coasts of the Americas as a result of poor gene flow. Fellaster zelandiae has a longer larval development time of 28 days than the development time in the other sand dollar genera (5–13 days; Emlet et al. 1987; Herrera et al. 1996), which provides for a greater potential dispersal distance. Similar levels of population connectivity to Fellaster zelandiae are seen only in one other sand dollar species, Clypeaster rosaceus (Zigler et al. 2008). Clypeaster rosaceus is one of the few species of echinoderm with a facultative planktotrophic larvae, providing a longer larval period than for typical echinoderm species (Emlet 1986b). Similarities in population homogeneity and larval dispersal times in Clypeaster rosaceus, Evechinus chloroticus and Fellaster zelandiae indicate that medium-to-long development times drive connectivity within regions.
We assume from the homogeneity of the GBS results that the lack of variation is due to ongoing gene flow. However, an alternative is that New Zealand sand dollar populations suffered population extirpations sometime in the past, and have had a recent population expansion. Habitat loss, such as what may occur during sea level drop associated with the last glacial maxima c. 20,000 years ago, could have affected Fellaster zelandiae population ranges and sizes in the past. However, seeing the similarities in the population homogeneity of Evechinus chloroticus and Fellaster zelandiae, two species with very similar larval developments and planktonic larval durations but distinct habitat requirements within shallow coastal ecosystems, makes the scenario of local extinction and then recolonisation for both species less likely.
Future genetic connectivity
The extent of the genetic homogeneity of Fellaster zelandiae as an echinoderm species that lives across such a large gradient may give insight into how gene flow occurs in long larval-dispersal species compared with shorter larval-dispersal species such as tropical echinoderms, and how gene flow may ameliorate climate change. Changing environmental conditions in the global oceans have predicted, but largely unquantified, negative implications for the survival of many marine species. Future ocean conditions (FOC) are expected and include changes to pH, temperature, primary productivity and hydrology, and Fellaster zelandiae populations currently occur in a gradient of all these variables. Phenotypic plasticity currently seen in this species may posit high adaptation potential of this species, so long as gene flow remains the same.
One impact of FOC on Fellaster zelandiae may be a decrease in larval thermal windows and shortening of the dispersal time because of the positive effects of moderate warming and increases in water column productivity predicted for New Zealand coastal waters (Law et al. 2018). This has been reported for other species that encounter warmer (García et al. 2015a, 2015b; Cui et al. 2024) and more productive environments (Emlet 1986a). Fellaster zelandiae currently experiences a 28-day larval phase, in which time it could disperse across regions along the coast; however, studies of F. zelandiae larvae raised in FOC decreased the development window (Dixon-Anderson 2025). Recently, potential larval dispersal (PLD) modelling across New Zealand for a 30-day dispersal window (similar to the development window of F. zelandiae) found a maximal dispersal distance of 400 km, but a mean dispersal distance of only 30 km (Michie et al. 2024). Larval connectivity among populations of different geographic regions can occur in 30-day dispersal models, but these predictions are relative to the strength and direction of the currents (Chiswell and Rickard 2011). In a few locations, such as the eastern coast of the South Island, larval dispersal occurred in a biased direction (i.e. northward), consistent with other marine taxa (Collins et al. 2010). In calm location embayments, eddies and weak currents may confine dispersal to a small region, resulting in the majority of recruitment being local. Thus, currents are a key driver in range sizes and changes to genetic connectivity in F. zelandiae. Because Michie et al. (2024) found that 7- and 14-day PLD had limited larval exchange among modelled locations, the shortening of larval windows for F. zelandiae may have important consequences on its population biology. This may indicate that genetic connectivity among populations that live at either extreme of these environments may weaken and diverge. Because this research has found the subtle hydrographic and geographic breaks that currently provide the genetic diversity (Table S1), we expect these breaks to widen and reduce the gene flow that occurs across them. As the majority of locations were seen to self-seed in each duration of model (Michie et al. 2024), it can be inferred that most populations are not reliant on external spawning for sustaining populations. This is a positive outlook, because no populations of F. zelandiae are in danger of extinction from genetic recession, merely that genetic homogeneity is at risk. Re-assessing the population genetics of F. zelandiae in the future will elucidate how larval ranges and biogeographical processes have been altered over geographic and temporal stretches.
Data availability
COI sequences are accessible in GenBank under the following accession numbers: PX096134–PX096139. GBS datasets generated or analysed during the current study are available in the BioSample database under Accession numbers SAMN50484970–SAMN50485130.
Conflicts of interest
The authors have no relevant financial or non-financial conflicts of interests to disclose.
Declaration of funding
C. I. Fraser was supported by a Royal Society of New Zealand Rutherford Discovery Fellowship (RDF-UOO1803), which provided some laboratory costs for this work. Genomic laboratory work was supported by Miles Lamare and the Department of Marine Science at the University of Otago.
Author contributions
I. S. Dixon-Anderson, C. I. Fraser and M. D. Lamare contributed to the study conception and design. Material preparation, data collection and analysis were performed by I. S. Dixon-Anderson. The first draft of the manuscript was written by I. S. Dixon-Anderson. I. S. Dixon-Anderson, C. I. Fraser and M. D. Lamare commented on previous versions of the manuscript and approved of the final version. C. I. Fraser and M. D. Lamare provided supervision of the project.
Acknowledgements
The authors thank Ian Hawes, Bill Dickson, Mark Elder, Adelle Heineman, Will Pinfold, Lily Bentall, Savannah Hori Te Pa, Courtney Butcher, Jess Moffitt and Duncan Campbell for aid in fieldwork. We acknowledge Sara Ferreira, Vahid Sepahvand and Pluto Liu for their assistance with laboratory procedures. We are grateful to AgResearch for preparation and sequencing of GBS libraries.
References
Alloway BV, Lowe DJ, Barrell DJA, Newnham RM, Almond PC, Augustinus PC, Bertler NAN, Carter L, Litchfield NJ, McGlone MS, Shulmeister J, Vandergoes MJ, Williams PW, NZ-INTIMATE members (2007) Towards a climate event stratigraphy for New Zealand over the past 30,000 years (NZ-INTIMATE project). Journal of Quaternary Science 22, 9-35.
| Crossref | Google Scholar |
Alvarez-Costes S, Baker CS, Constantine R, Carroll EL, Guhlin J, Dutoit L, Ferreira S, Heimeier D, Gemmell NJ, Gillum J, Hamner RM, Rayment W, Roe W, Te Aikā B, Urban L, Alexander A (2025) Leveraging synteny to generate reference genomes for conservation: assembling the genomes of Hector’s and Māui Dolphins. Molecular Ecology Resources e14109.
| Crossref | Google Scholar |
Apte S, Gardner JPA (2002) Population genetic subdivision in the New Zealand greenshell mussel (Perna canaliculus) inferred from single-strand conformation polymorphism analysis of mitochondrial DNA. Molecular Ecology 11, 1617-1628.
| Crossref | Google Scholar | PubMed |
Arranz V, Thakur V, Lavery SD (2021) Demographic history, not larval dispersal potential, explains differences in population structure of two New Zealand intertidal species. Marine Biology 168, 105.
| Crossref | Google Scholar |
Ayers KL, Waters JM (2005) Marine biogeographic disjunction in central New Zealand. Marine Biology 147, 1045-1052.
| Crossref | Google Scholar |
Banks SC, Ling SD, Johnson CR, Piggott MP, Williamson JE, Beheregaray LB (2010) Genetic structure of a recent climate change-driven range extension. Molecular Ecology 19, 2011-2024.
| Crossref | Google Scholar | PubMed |
Barker MF (2013) Chapter 24 – Evechinus chloroticus. In ‘Sea urchins: biology and ecology. Developments in Aquaculture and Fisheries Science, vol. 38’. (Ed. JM Lawrence) pp. 355–368. (Elsevier) doi:10.1016/B978-0-12-396491-5.00024-1
Beheregaray LB (2008) Twenty years of phylogeography: the state of the field and the challenges for the southern hemisphere. Molecular Ecology 17, 3754-3774.
| Crossref | Google Scholar | PubMed |
Bermingham E, Lessios HA (1993) Rate variation of protein and mitochondrial DNA evolution as revealed by sea urchins separated by the isthmus of Panama. Proceedings of the National Academy of Sciences 90, 2734-2738.
| Crossref | Google Scholar |
Bosch I, Beauchamp KA, Steele ME, Pearse JS (1987) Development, metamorphosis, and seasonal abundance of embryos and larvae of the antarctic sea urchin Sterechinus neumayeri. The Biological Bulletin 173, 126-135.
| Crossref | Google Scholar | PubMed |
Bronstein O, Kroh A, Tautscher B, Liggins L, Haring E (2017) Cryptic speciation in pan-tropical sea urchins: a case study of an edge-of-range population of Tripneustes from the Kermadec Islands. Scientific Reports 7, 5948.
| Crossref | Google Scholar | PubMed |
Chen B-Y, Chen C-P (1993) Reproduction and development of a Miniature Sand Dollar, Sinaechinocyamus mai (Echinodermata: Echinoidea) in Taiwan. Bulletin of the Institute of Zoology, Academia Sinica 32, 100-110.
| Google Scholar |
Chiswell SM, Booth JD (2008) Sources and sinks of larval settlement in Jasus edwardsii around New Zealand: where do larvae come from and where do they go? Marine Ecology Progress Series 354, 201-217.
| Crossref | Google Scholar |
Chiswell SM, Rickard GJ (2011) Larval connectivity of harbours via ocean currents: a New Zealand study. Continental Shelf Research 31, 1057-1074.
| Crossref | Google Scholar |
Chiswell SM, Wilkin J, Booth JD, Stanton B (2003) Trans-Tasman Sea larval transport: is Australia a source for New Zealand rock lobsters? Marine Ecology Progress Series 247, 173-182.
| Crossref | Google Scholar |
Chiswell SM, Stevens CL, Macdonald HS, Grant BS, Price O (2021) Circulation in Tasman–Golden Bays and Greater Cook Strait, New Zealand. New Zealand Journal of Marine and Freshwater Research 55, 223-248.
| Crossref | Google Scholar |
Collins CJ, Fraser CI, Ashcroft A, Waters JM (2010) Asymmetric dispersal of southern bull-kelp (Durvillaea antarctica) adults in coastal New Zealand: testing an oceanographic hypothesis. Molecular Ecology 19, 4572-4580.
| Crossref | Google Scholar | PubMed |
Coppard SE, Lessios HA (2017) Phylogeography of the sand dollar genus Encope: implications regarding the Central American Isthmus and rates of molecular evolution. Scientific Reports 7, 11520.
| Crossref | Google Scholar | PubMed |
Coppard SE, Zigler KS, Lessios HA (2013) Phylogeography of the sand dollar genus Mellita: cryptic speciation along the coasts of the Americas. Molecular Phylogenetics and Evolution 69, 1033-1042.
| Crossref | Google Scholar | PubMed |
Costello MJ, Tsai P, Wong PS, Cheung AKL, Basher Z, Chaudhary C (2017) Marine biogeographic realms and species endemicity. Nature Communications 8, 1057.
| Crossref | Google Scholar | PubMed |
Cresswell G (2000) Currents of the continental shelf and upper slope of Tasmania. Papers and Proceedings of the Royal Society of Tasmania 133, 21-30.
| Crossref | Google Scholar |
Cui D, Zou W, Wu B, Jiao R, Zhang S, Zhao T, Zhan Y, Chang Y (2024) Interactive effects of chronic ocean acidification and warming on the growth, survival, and physiological responses of adults of the temperate sea urchin Strongylocentrotus intermedius. Chemosphere 356, 141907.
| Crossref | Google Scholar | PubMed |
Dodds KG, McEwan JC, Brauning R, Anderson RM, van Stijn TC, Kristjánsson T, Clarke SM (2015) Construction of relatedness matrices using genotyping-by-sequencing data. BMC Genomics 16, 1047.
| Crossref | Google Scholar | PubMed |
Dohner M, Phillips NE, Ritchie PA (2018) Fine-scale genetic structure across a New Zealand disjunction for the direct-developing intertidal whelk Cominella maculosa (Gastropoda: Buccinidae). Biological Journal of the Linnean Society 123, 593-602.
| Crossref | Google Scholar |
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379.
| Crossref | Google Scholar | PubMed |
Emerson BC, Hewitt GM (2005) Phylogeography. Current Biology 15, R367-R371.
| Crossref | Google Scholar | PubMed |
Emlet RB (1986a) Larval production, dispersal, and growth in a fjord: a case study on larvae of the sand dollar Dendraster excentricus. Marine Ecology Progress Series 31, 245-254.
| Crossref | Google Scholar |
Emlet RB (1986b) Facultative planktotrophy in the tropical echinoid Clypeaster rosaceus (Linnaeus) and a comparison with obligate planktotrophy in Clypeaster subdepressus (Gray) (Clypeasteroida: Echinoidea). Journal of Experimental Marine Biology and Ecology 95, 183-202.
| Crossref | Google Scholar |
Endo M, Hirose M, Honda M, Koga H, Morino Y, Kiyomoto M, Wada H (2018) Hidden genetic history of the Japanese sand dollar Peronella (Echinoidea: Laganidae) revealed by nuclear intron sequences. Gene 659, 37-43.
| Crossref | Google Scholar | PubMed |
Farquhar H (1894) Notes on New Zealand Echinoderms. Transactions and Proceedings of the Royal Society of New Zealand 27, 194-208.
| Google Scholar |
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
| Crossref | Google Scholar | PubMed |
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294-299.
| Google Scholar | PubMed |
Foltz DW, Nguyen AT, Kiger JR, Mah CL (2008) Pleistocene speciation of sister taxa in a North Pacific clade of brooding sea stars (Leptasterias). Marine Biology 154, 593-602.
| Crossref | Google Scholar |
Foster RJ, Philip GM (1980) Some Australian Late Cainozoic Echinoids. Proceedings of the Royal Society of Victoria 91(2), 155-160.
| Crossref | Google Scholar |
Francis RM (2017) pophelper: an R package and web app to analyse and visualize population structure. Molecular Ecology Resources 17, 27-32.
| Crossref | Google Scholar | PubMed |
Fraser CI, McGaughran A, Chuah A, Waters JM (2016) The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages. Molecular Ecology 25, 3683-3695.
| Crossref | Google Scholar | PubMed |
Frichot E, François O (2015) LEA: an R package for landscape and ecological association studies. Methods in Ecology and Evolution 6, 925-929.
| Crossref | Google Scholar |
García E, Clemente S, Hernández JC (2015a) Ocean warming ameliorates the negative effects of ocean acidification on Paracentrotus lividus larval development and settlement. Marine Environmental Research 110, 61-68.
| Crossref | Google Scholar |
García E, Clemente S, López C, McAlister JS, Hernández JC (2015b) Ocean warming modulates the effects of limited food availability on Paracentrotus lividus larval development. Marine Biology 162, 1463-1472.
| Crossref | Google Scholar |
Gemmell MR, Trewick SA, Crampton JS, Vaux F, Hills SFK, Daly EE, Marshall BA, Beu AG, Morgan-Richards M (2018) Genetic structure and shell shape variation within a rocky shore whelk suggest both diverging and constraining selection with gene flow. Biological Journal of the Linnean Society 125, 827-843.
| Crossref | Google Scholar |
Gillespie RG, Baldwin BG, Waters JM, Fraser CI, Nikula R, Roderick GK (2012) Long-distance dispersal: a framework for hypothesis testing. Trends in Ecology & Evolution 27, 47-56.
| Crossref | Google Scholar | PubMed |
Goldstien SJ, Schiel DR, Gemmell NJ (2006) Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand. Molecular Ecology 15, 3259-3268.
| Crossref | Google Scholar | PubMed |
Gonzalez-Bernat MJ, Lamare M, Uthicke S, Byrne M (2013) Fertilisation, embryogenesis and larval development in the tropical intertidal sand dollar Arachnoides placenta in response to reduced seawater pH. Marine Biology 160, 1927-1941.
| Crossref | Google Scholar |
Gordon DP, Beaumont J, MacDiarmid A, Robertson DA, Ahyong ST (2010) Marine Biodiversity of Aotearoa New Zealand. PLoS ONE 5, e10905.
| Crossref | Google Scholar | PubMed |
Grkovic T, Copp BR (2013) Establishment of a phenotypic-based sand dollar Fellaster zelandiae embryo development assay and its application in defining the structure–activity relationship of discorhabdin alkaloids. Natural Product Communications 8, 1934578X1300800604.
| Crossref | Google Scholar |
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59, 307-321.
| Crossref | Google Scholar | PubMed |
Halbritter AH, Billeter R, Edwards PJ, Alexander JM (2015) Local adaptation at range edges: comparing elevation and latitudinal gradients. Journal of Evolutionary Biology 28, 1849-1860.
| Crossref | Google Scholar | PubMed |
Hasegawa M, Kishino H, Yano T (1985) Dating of the human–ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22, 160-174.
| Crossref | Google Scholar | PubMed |
Hayes DE, Ringis J (1973) Seafloor spreading in the Tasman Sea. Nature 243, 454-458.
| Crossref | Google Scholar |
Herrera JC, McWeeney SK, McEdward LR (1996) Diversity of energetic strategies among echinoid larvae and the transition from feeding to nonfeeding development. Oceanologica Acta 19, 313-321.
| Google Scholar |
Hoegh-Guldberg O, Pearse JS (1995) Temperature, food availability, and the development of marine invertebrate larvae. American Zoologist 35, 415-425.
| Crossref | Google Scholar |
Holmes F (1987) A brief review of Australian Tertiary Echinoids. MAPS Digest 10(5), 79-88.
| Google Scholar |
Hopkins JE, Shaw AGP, Challenor P (2010) The Southland Front, New Zealand: variability and ENSO correlations. Continental Shelf Research 30, 1535-1548.
| Crossref | Google Scholar |
Huanel OR, Nelson WA, Robitzch V, Mauger S, Faugeron S, Preuss M, Zuccarello GC, Guillemin M-L (2020) Comparative phylogeography of two Agarophyton species in the New Zealand archipelago. Journal of Phycology 56, 1575-1590.
| Crossref | Google Scholar | PubMed |
Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403-1405.
| Crossref | Google Scholar | PubMed |
Kamvar ZN, Tabima JF, Grünwald NJ (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2, e281.
| Crossref | Google Scholar | PubMed |
Kamvar ZN, Brooks JC, Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics 6, 208.
| Crossref | Google Scholar |
Karelitz SE, Uthicke S, Foo SA, Barker MF, Byrne M, Pecorino D, Lamare MD (2017) Ocean acidification has little effect on developmental thermal windows of echinoderms from Antarctica to the tropics. Global Change Biology 23, 657-672.
| Crossref | Google Scholar | PubMed |
Katoh K (Ed.) (2021) ‘Multiple sequence alignment: methods and protocols. Methods in Molecular Biology, vol. 2231.’ (Springer: New York, NY, USA) doi:10.1007/978-1-0716-1036-7
Kearse M, Moir A, Wilson R, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12), 1647-1649.
| Crossref | Google Scholar |
Knapp M, Mudaliar R, Havell D, Wagstaff SJ, Lockhart PJ (2007) The drowning of New Zealand and the problem of Agathis. Systematic Biology 56, 862-870.
| Crossref | Google Scholar | PubMed |
Knaus BJ, Grünwald NJ (2017) vcfR: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources 17, 44-53.
| Crossref | Google Scholar | PubMed |
Kumar R, Kumar V (2018) A review of phylogeography: biotic and abiotic factors. Geology, Ecology, and Landscapes 2, 268-274.
| Crossref | Google Scholar |
Lamare MD (1998) Origin and transport of larvae of the sea urchin Evechinus chloroticus (Echinodermata: Echinoidea) in a New Zealand fiord. Marine Ecology Progress Series 174, 107-121.
| Crossref | Google Scholar |
Law CS, Rickard GJ, Mikaloff-Fletcher SE, Pinkerton MH, Behrens E, Chiswell SM, Currie K (2018) Climate change projections for the surface ocean around New Zealand. New Zealand Journal of Marine and Freshwater Research 52, 309-335.
| Crossref | Google Scholar |
Lee H, Lin J-P, Li H-C, Chang L-Y, Lee K-S, Lee S-J, Chen W-J, Sankar A, Kang S-C (2019) Young colonization history of a widespread sand dollar (Echinodermata; Clypeasteroida) in western Taiwan. Quaternary International 528, 120-129.
| Crossref | Google Scholar |
Lee H, Lee K-S, Hsu C-H, Lee C-W, Li C-E, Wang J-K, Tseng C-C, Chen W-J, Horng C-C, Ford CT, Kroh A, Bronstein O, Tanaka H, Oji T, Lin J-P, Janies D (2023) Phylogeny, ancestral ranges and reclassification of sand dollars. Scientific Reports 13, 10199.
| Crossref | Google Scholar | PubMed |
Lefort V, Longueville J-E, Gascuel O (2017) SMS: Smart Model Selection in PhyML. Molecular Biology and Evolution 34, 2422-2424.
| Crossref | Google Scholar | PubMed |
Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Boehm JT, Machida RJ (2013) A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Frontiers in Zoology 10, 34.
| Crossref | Google Scholar | PubMed |
Lessios HA (2008) The Great American Schism: divergence of marine organisms after the rise of the central American Isthmus. Annual Review of Ecology, Evolution, and Systematics 39, 63-91.
| Crossref | Google Scholar |
Lessios HA, Kessing BD, Robertson DR, Paulay G (1999) Phylogeography of the pantropical sea urchin Eucidaris in relation to land barriers and ocean currents. Evolution 53, 806-817.
| Crossref | Google Scholar | PubMed |
Lo Brutto S, Arculeo M, Stewart Grant W (2011) Climate change and population genetic structure of marine species. Chemistry and Ecology 27, 107-119.
| Crossref | Google Scholar |
Loeza-Quintana T, Carr CM, Khan T, Bhatt YA, Lyon SP, Hebert PDN, Adamowicz SJ (2019) Recalibrating the molecular clock for Arctic marine invertebrates based on DNA barcodes. Genome 62, 200-216.
| Crossref | Google Scholar | PubMed |
Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics 9, e1003215.
| Crossref | Google Scholar | PubMed |
Michie C, Lundquist CJ, Lavery SD, Della Penna A (2024) Spatial and temporal variation in the predicted dispersal of marine larvae around coastal Aotearoa New Zealand. Frontiers in Marine Science 10, 1292081.
| Crossref | Google Scholar |
Mladenov PV, Allibone RM, Wallis GP (1997) Genetic differentiation in the New Zealand sea urchin Evechinus chloroticus (Echinodermata: Echinoidea). New Zealand Journal of Marine and Freshwater Research 31, 261-269.
| Crossref | Google Scholar |
Nazareno AG, Bemmels JB, Dick CW, Lohmann LG (2017) Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Molecular Ecology Resources 17, 1136-1147.
| Crossref | Google Scholar | PubMed |
Nodder SD, Pilditch CA, Probert PK, Hall JA (2003) Variability in benthic biomass and activity beneath the Subtropical Front, Chatham Rise, SW Pacific Ocean. Deep-Sea Research – I. Oceanographic Research Papers 50, 959-985.
| Crossref | Google Scholar |
Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M (2014) VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. Bioinformatics 30, 2076-2078.
| Crossref | Google Scholar | PubMed |
Ovenden JR, Brasher DJ, White RWG (1992) Mitochondrial DNA analyses of the red rock lobster Jasus edwardsii supports an apparent absence of population subdivision throughout Australasia. Marine Biology 112, 319-326.
| Crossref | Google Scholar |
Padovan A, Chick RC, Cole VJ, Dutoit L, Hutchings PA, Jack C, Fraser CI (2020) Genomic analyses suggest strong population connectivity over large spatial scales of the commercially important baitworm, Australonuphis teres (Onuphidae). Marine and Freshwater Research 71, 1549-1556.
| Crossref | Google Scholar |
Palumbi SR (1996) What can molecular genetics contribute to marine biogeography? An urchin’s tale. Journal of Experimental Marine Biology and Ecology 203, 75-92.
| Crossref | Google Scholar |
Pecorino D, Lamare MD, Barker MF, Byrne M (2013) How does embryonic and larval thermal tolerance contribute to the distribution of the sea urchin Centrostephanus rodgersii (Diadematidae) in New Zealand? Journal of Experimental Marine Biology and Ecology 445, 120-128.
| Crossref | Google Scholar |
Rocha LA, Bernal MA, Gaither MR, Alfaro ME (2013) Massively parallel DNA sequencing: the new frontier in biogeography. Frontiers of Biogeography 5, 67-77.
| Crossref | Google Scholar |
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61, 539-542.
| Crossref | Google Scholar | PubMed |
Ross PM, Hogg ID, Pilditch CA, Lundquist CJ (2009) Phylogeography of New Zealand’s coastal benthos. New Zealand Journal of Marine and Freshwater Research 43, 1009-1027.
| Crossref | Google Scholar |
Sadler T, Pledge N (1985) The fossil sea urchin Fellaster incisa – an extension of range. Transactions and Proceedings of the Royal Society of South Australia 109, 175-176.
| Google Scholar |
Shanks AL (2009) Pelagic larval duration and dispersal distance revisited. The Biological Bulletin 216, 373-385.
| Crossref | Google Scholar | PubMed |
Sievers F, Higgins DG (2021) The Clustal Omega multiple alignment package. In ‘Multiple sequence alignment. Methods in Molecular Biology, vol. 2231’. (Ed. K Katoh) pp 3–16. (Humana: New York, NY, USA) 10.1007/978-1-0716-1036-7_1
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7, 539.
| Crossref | Google Scholar | PubMed |
Soars NA, Prowse TAA, Byrne M (2009) Overview of phenotypic plasticity in echinoid larvae, ‘Echinopluteus transversus’ type vs. typical echinoplutei. Marine Ecology Progress Series 383, 113-125.
| Crossref | Google Scholar |
Strathmann RR (1974) Introduction to function and adaptation in echinoderm larvae. Thalassia Jugoslavica 10(1–2), 321-339.
| Google Scholar |
Strathmann RR (1978) Length of pelagic period in echinoderms with feeding larvae from the Northeast Pacific. Journal of Experimental Marine Biology and Ecology 34, 23-27.
| Crossref | Google Scholar |
Sutton PJH (2003) The Southland Current: a subantarctic current. New Zealand Journal of Marine and Freshwater Research 37, 645-652.
| Crossref | Google Scholar |
Thomas LJ, Liggins L, Banks SC, Beheregaray LB, Liddy M, McCulloch GA, Waters JM, Carter L, Byrne M, Cumming RA, Lamare MD (2021) The population genetic structure of the urchin Centrostephanus rodgersii in New Zealand with links to Australia. Marine Biology 168, 138.
| Crossref | Google Scholar |
Trewick SA, Bland KJ (2012) Fire and slice: palaeogeography for biogeography at New Zealand’s North Island/South Island juncture. Journal of the Royal Society of New Zealand 42, 153-183.
| Crossref | Google Scholar |
Vaux F, Dutoit L, Fraser CI, Waters JM (2023) Genotyping-by-sequencing for biogeography. Journal of Biogeography 50, 262-281.
| Crossref | Google Scholar |
Walton K, Marshall BA, Phillips NE, Verry AJF, Ritchie PA (2019) Phylogeography of the New Zealand whelks Cominella maculosa and C. virgata (Gastropoda: Neogastropoda: Buccinoidea: Buccinidae). Biological Journal of the Linnean Society 126, 178-202.
| Crossref | Google Scholar |
Ward RD, Holmes BH, O’hara TD (2008) DNA barcoding discriminates echinoderm species. Molecular Ecology Resources 8, 1202-1211.
| Crossref | Google Scholar | PubMed |
Waters JM, Craw D (2006) Goodbye Gondwana? New Zealand biogeography, geology, and the problem of circularity. Systematic Biology 55, 351-356.
| Crossref | Google Scholar | PubMed |
Waters JM, Roy MS (2004) Phylogeography of a high-dispersal New Zealand sea-star: does upwelling block gene-flow? Molecular Ecology 13, 2797-2806.
| Crossref | Google Scholar | PubMed |
Waters JM, McCulloch GA, Eason JA (2007) Marine biogeographical structure in two highly dispersive gastropods: implications for trans-Tasman dispersal. Journal of Biogeography 34, 678-687.
| Crossref | Google Scholar |
Weissel JK, Hayes DE (1977) Evolution of the Tasman Sea reappraised. Earth and Planetary Science Letters 36, 77-84.
| Crossref | Google Scholar |
Wickham H (2016) ‘ggplot2: Elegant Graphics for Data Analysis.’ (Springer International Publishing: Cham, Switzerland) doi:10.1007/978-3-319-24277-4
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012) A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326-3328.
| Crossref | Google Scholar | PubMed |
Zigler KS, Lessios HA, Raff RA (2008) Egg energetics, fertilization kinetics, and population structure in echinoids with facultatively feeding larvae. The Biological Bulletin 215, 191-199.
| Crossref | Google Scholar | PubMed |