Matthew Iacchei | University of Hawaii at Manoa (original) (raw)

Papers by Matthew Iacchei

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marin... more The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.

Large population sizes and high dispersal potential should lead to temporal genetic stability in ... more Large population sizes and high dispersal potential should lead to temporal genetic stability in marine species; however, the magnitude of allele frequency shifts through time have varied greatly in prior studies. We investigated temporal variation in the genetic composition of populations of two planktonic copepod species at an open ocean time series site in the North Pacific Subtropical Gyre (Station ALOHA, 22.458 N, 158.8 W). We sequenced fragments of the mitochondrial genes cytochrome c oxidase subunit II (Haloptilus longicornis) and subunit I (Pleuromamma xiphias) from approximately 500 individuals of each species collected on 11 cruises from September 2012 to October 2013 (12–15 generations). Conventional population genetic analyses found no evidence for significant temporal variation across cruises, including results of non-hierarchical analysis of molecular variance, pairwise Fst values among cruises, and isolation-by-time Mantel tests. Generalized entropies were able to characterize the turnover of rare haplotypic variants through time using q = 0 (haplotype richness), the shifting frequencies of the less common haplotypes using q = 1 (Shannon differentiation), and the general stability of the most abundant haplotypes using q = 2 (Jost's D). With q = 1, mild seasonality was detected in the composition of P. xiphias haplotypes from three summertime cruises, in which both copepodites and adults were included in the analyses. These results highlight the complementary insights that F-statistics and generalized entropy contribute to characterizing the nuances of population genetic composition through time. This approach may prove particularly useful for unlocking patterns in genomic datasets for marine species.

Aim To resolve phylogeographical partitions in the pronghorn spiny lobster, Panulirus penicillatu... more Aim To resolve phylogeographical partitions in the pronghorn spiny lobster, Panulirus penicillatus, which has a nine-month pelagic larval phase and the broadest distribution among spiny lobsters. With samples from the Red Sea to the East Pacific, we test genetic partitions across two-thirds of the planet, in a species with one of the longest pelagic phases. Location Red Sea, Indian and Pacific Oceans. Methods A fragment of the mtDNA cytochrome c oxidase subunit I gene (COI) was resolved in 774 individuals from 28 locations, plus 55 sequences (10 locations) from public databases. Portions of COI, 12S and 16S mtDNA regions were resolved for phylogenetic analyses on a subset of individuals. Phy-logenetic and population-level analyses were used to detect evolutionary partitions and dispersal barriers. Results Significant population structuring was detected (overall Φ ST = 0.310, P < 0.001). Samples from the Red Sea and East Pacific Provinces (western and eastern range edges) comprise distinct phylogenetic lineages, divergent at d = 1.1% and 1.8%, respectively, from the Indo-Pacific. Coalescent analyses indicate a Pleistocene isolation for the Red Sea (0.71 Ma) and East Pacific (1.52 Ma). Excluding the Red Sea and East Pacific, structure across the rest of the range was comparatively low, but significant (Φ ST = 0.018, P < 0.001). Main conclusions The Red Sea and East Pacific populations are phylogeneti-cally distinct from populations elsewhere in the range. The East Pacific population diverged earliest, and may represent a distinct subspecies. Phylogeographical divisions align with the major Indo-Pacific biogeographical barriers, and with subsets of provincial designations from two frameworks: one based on levels of endemism and one on species composition. Tropical and temperate regions in the Pacific are significantly differentiated, potentially indicating an ecological partition. Isolation at eastern and western peripheral provinces may serve as a starting point for evolutionary diversification within this group.

Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to... more Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions.

Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity... more Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of bio-geographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phy-logeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semi-isolated) divergences within provinces and biodiversity hotspots.

Journal of Marine Biology, Jan 1, 2011

Seascape genetics, a term coined in 2006, is a fast growing area of population genetics that draw... more Seascape genetics, a term coined in 2006, is a fast growing area of population genetics that draws on ecology, oceanography and geography to address challenges in basic understanding of marine connectivity and applications to management. We provide an accessible overview of the latest developments in seascape genetics that merge exciting new ideas from the field of marine population connectivity with statistical and technical advances in population genetics. After summarizing the historical context leading to the emergence of seascape genetics, we detail questions and methodological approaches that are evolving the discipline, highlight applications to conservation and management, and conclude with a summary of the field's transition to seascape ge-nomics. From 100 seascape genetic studies, we assess trends in taxonomic and geographic coverage, sampling and statistical design, and dominant seascape drivers. Notably, temperature, oceanography and geography show equal prevalence of influence on spatial genetic patterns, and tests of over 20 other seascape factors suggest that a variety of forces impact connec-tivity at distinct spatio-temporal scales. A new level of rigor in statistical analysis is critical for disentangling multiple drivers and spurious effects. Coupled with GIS data and genomic scale sequencing methods, this rigor is taking seascape genetics beyond an initial focus on identifying correlations to hypothesis-driven insights into patterns and processes of population An underwater seascape from the top of Steve's Bommie in the Great Barrier Reef, Australia. Photo by Jonathan B. Puritz OPEN PEN ACCESS CCESS connectivity and adaptation. The latest studies are illuminating differences between demographic, functional and neutral genetic connectivity, and informing applications to marine reserve design, fisheries science and strategies to assess resilience to climate change and other anthropogenic impacts.

International cooperation is essential to effectively manage fisheries species whose ranges do no... more International cooperation is essential to effectively manage fisheries species whose ranges do not adhere to geopolitical borders. The California spiny lobster, Panulirus interruptus is fished commercially and recreationally throughout its range from Baja Magdalena, Mexico to Point Conception, California. Previous studies provide indirect evidence that California lobster populations may receive a substantial number of recruits from populations in northern and central Baja. We used a 494-base-pair fragment of the cytochrome oxidase I region of the mitochondrial DNA genome, and 7 nuclear microsatellite markers to investigate whether lobster populations in California are locally self-seeding or rely on cross-border recruitment to persist. We genotyped 989 samples from 17 populations throughout the range of P. interruptus, and found significant structure exists among populations, but with low spatial signal (fst = 0.006, p = 0.001; Fst = 0.004, p < 0.0001). These results are surprisi...

Background/Question/Methods Despite debates regarding the extent and severity of species declines... more Background/Question/Methods Despite debates regarding the extent and severity of species declines, there is overwhelming consensus that human impacts on marine ecosystems have decreased individual abundance and altered the size structure of harvested species worldwide. However, few studies have examined the concomitant changes in the communities in which these fisheries species reside. In this study, we experimentally simulate two commonly used fisheries management strategies (size limits and total allowable catch or bag limits) to investigate how they impact ecological community structure when applied in a controlled setting. Our focal species, yellowfoot ‘opihi (Cellana sandwicensis) is the most prized of three congeneric limpet species endemic to Hawai‘i. All three species are harvested commercially, recreationally, and for subsistence, and are currently regulated with a minimum size limit. To determine the different impacts that regulations of size versus overall catch may have ...

Molecular ecology, 2014

What shapes variation in genetic structure within a community of codistributed species is a centr... more What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R2=0.22), but accounting for higher FST values...

Proceedings of the 29th American Academy …, 2010

ABSTRACT The Papah

ABSTRACT Background/Question/Methods Understanding how environmental variables at multiple scales... more ABSTRACT Background/Question/Methods Understanding how environmental variables at multiple scales influence the structure of stream fish assemblages is important for habitat assessment, stream restoration, and for predicting responses to environmental change. A focus on the functional structure of species assemblages in relation to environmental gradients may reveal more general patterns applicable across geographic regions. In this study, we used functional traits related to the trophic ecology, habitat use, and life-history strategies of fishes to examine the influences of environmental factors on stream fish assemblages in the Brazos and Trinity river basins in Central Texas. Relationships between functional structure of assemblages and environmental factors at local, landscape, and regional scales were examined. We also identified associations between functional diversity of fish assemblages and established measures of biotic integrity and habitat quality. Results/Conclusions Environmental characteristics at all three scales influenced the functional attributes of assemblages studied here. At the local reach scale, stream size, substrate characteristics, the availability of riffle and pool habitats, and abundance of in-stream cover structures were related to the functional trait composition of fish assemblages. Landscape features most strongly related to functional structure were the extent of forested area in the watershed and the amount of land developed for urban and agricultural uses. At the regional scale, broad physiographic differences between ecoregions had a large influence on the taxonomic and functional composition of stream fish assemblages in Central Texas. In general, the functional trait-space occupied by fish assemblages was greatest in streams with high habitat quality scores located within landscapes with less alteration for agriculture and urban development. Currently used indices of biotic integrity incorporate some functional aspects of fish assemblage structure (e.g., trophic guilds, pollution tolerance categories), but identifying specific functional traits or suites of traits related to stream habitat quality could potentially improve on these approaches and provide more sensitive and broadly applicable metrics.

Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium, 2010

Since the arrival of the first Polynesian voyagers to the Hawaiian archipelago, spiny lobsters ha... more Since the arrival of the first Polynesian voyagers to the Hawaiian archipelago, spiny lobsters have proved to be valuable fisheries species in Hawai 'i. However, the combination of longterm commercial and recreational fisheries for this species, and changing environmental conditions, have led to declining catch rates since the 1950s. The Papahānaumokuākea Marine National Monument (PMNM), established in 2006, now provides an extensive harvest refuge area for lobster species in the Northwest Hawaiian ...

New Zealand Journal of …, Jan 1, 2005

The California spiny or red rock lobster, Panulirus interruptus, is an ecologically and economica... more The California spiny or red rock lobster, Panulirus interruptus, is an ecologically and economically important species that has been exploited since the 1800s. No previous study in California has assessed the impacts of the recreational or commercial lobster harvest. Before the 2003-04 commercial and recreational lobster seasons, we conducted a fishery-independent trap survey at Santa Catalina Island to document the impact of the lobster fisheries on the size structure, abundance, and sex ratios of mature P. interruptus (>65 mm carapace length (CL)). We concurrently sampled a predominantly commercially fished area, a recreationally fished area, and a 23-year-old invertebrate no-take (INT) reserve. Relative to the INT reserve, legal-size lobsters in the recreational area were similar in CL, but 31% less abundant. Legal-size lobsters in the commercial area were 8% smaller and 70% less abundant than those in the INT reserve. The sex ratio of legal-size lobsters, although near 50:50 in the recreational and INT reserve areas, was male-dominated (67:33) in the commercial area. Differences in CPUE and mean CL of sub-legal lobsters in the recreational and commercial areas suggest that factors in addition to harvesting pressure may affect these populations. Total biomass of mature lobsters in the recreational and commercial areas was 92% and 45%, respectively, of biomass in the INT reserve. Fecundity in the recreational and commercial areas was 83% and 42%, respectively, of fecundity in the INT reserve. This study provides preliminary data for future ecological studies and fisheries management evaluations.

We compared mitochondrial genetic data for two spiny lobsters in Hawaii with different geographic... more We compared mitochondrial genetic data for two spiny lobsters in Hawaii with different geographic ranges and histories of fishing pressure. Panulirus marginatus (Quoy and Gaimard, 1825) is endemic to Hawaii, and experienced a short, intense fishery in the Northwestern Hawaiian Islands (NWHI) and long-term, less intense exploitation in the Main Hawaiian Islands (MHI). Populations show significant overall structure (F ST = 0.0037, P = 0.007; D est_Chao = 0.137), with regional differentiation (F CT = 0.002, P = 0.047) between the MHI and the NWHI. Haplotype diversity did not differ significantly between regions (F 2, 8 = 3.740, P = 0.071); however, nucleotide diversity is significantly higher at the primary NWHI fishery banks (0.030) than in the MHI (0.026, Tukey's P = 0.013). In contrast, Panulirus penicillatus (Olivier, 1791), found across the tropical Indo-West Pacific region, was not targeted by the NWHI fishery, but has experienced long-term exploitation in the MHI. Panulirus penicillatus has no significant overall population structure in Hawaii (F ST = 0.0083, P = 0.063; D est_Chao = 0.278), although regional differentiation (F CT = 0.0076, P = 0.0083) between the MHI and the NHWI is significant. Neither haplotype nor nucleotide diversity differed significantly between regions for P. penicillatus. While neither species has suffered a loss of genetic diversity from fishing, our results highlight that only by incorporating knowledge of fishing history with genetic connectivity data can we understand the most beneficial management strategy for each species. Neither exemplar species nor specific suites of traits are reliable predictors of the spatial scales of management.

We combine kinship estimates with traditional F-statistics to explain contemporary drivers of pop... more We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (Φ ST = 0.006, P = 0.001; D est_Chao = 0.025) and seven nuclear microsatellites (F ST = 0.004, P < 0.001; D est_Chao = 0.03), despite the species' 240-to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise F ST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F 16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D est_Chao , R 2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R 2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F ST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.

Molecular Ecology, Jan 1, 2010

Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed... more Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed as ‘chaotic’ genetic patchiness and ecologically uninformative. Here, using three datasets that individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet’s whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site-to-site migration probability derived from a high resolution multi-year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information–theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure.

Journal of Marine Biology, Jan 1, 2011

Molecular ecology, 2014

Proceedings of the 29th American Academy …, 2010

ABSTRACT The Papah

Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium, 2010

New Zealand Journal of …, Jan 1, 2005

Molecular Ecology, Jan 1, 2010