M.S. - Zoology

Permanent URI for this collectionhttps://hdl.handle.net/10125/2172

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From Seawater to Sequences: Environmental DNA Reveals Hidden Diversity of the Agariciidae Corals in Hawai‘i
(University of Hawai'i at Manoa, 2024) Vimond, Cecile; Marko, Peter; Zoology
Knowledge of coral species diversity, community structure, and function has traditionallyrelied on morphological variation to differentiate species. Yet, coral morphology and its relationship to species boundaries are notoriously difficult to understand, leading to both underand over- estimates of diversity. However, better molecular data have transformed our understanding of coral species boundaries. In the Agariciidae coral family, recent molecular research revealed numerous cryptic taxa within single widespread nominal species across the Indo-Pacific. This high diversity of morphologically cryptic taxa, combined with the ecologically cryptic nature of many agariciids, provides an ideal opportunity to test an environmental DNA (eDNA) approach to assess diversity in taxa that are both difficult to visually identify and sample. In the present study, the mitochondrial cox1-1-rRNA spacer was sequenced from water samples to evaluate agariciid distribution and diversity across 32 sites on four Main Hawaiian Islands. A total of 9 distinct clades of agariciids were detected, including several cryptic lineages within the nominal Pavona varians. This eDNA approach identified more taxa than are known from visual surveys conducted on shallow Hawaiian reefs. Significant differences in species richness and diversity were observed across islands and sites. Analysis of the effect of environmental variation on community composition identified three key factors shaping agariciid communities (rugosity, sedimentation, and temperature). Overall, this study demonstrates the power of eDNA to uncover hidden coral diversity and elucidate patterns and of species diversity and community composition among agariciids across the Hawaiian Islands.
The Landscape Genetics of Novel Environments: How Urban Environments Structure the Introduced Lizards of Honolulu
(University of Hawai'i at Manoa, 2023) Myers, Natalie A.; Thomson, Robert; Zoology
Globalization has led to the unintended introduction of non-native species to novel environments. The urban landscape presents new challenges and opportunities for introduced species, but there is a lack of understanding about how these species interact with the urban environment and the timing in which those impacts may begin to manifest in genetic patterns. Our study investigated the landscape genetics of three well-established introduced reptile species on Oahu, HI; Anolis sagrei, Hemidactylus frenatus, and Phelsuma laticauda, with the goal of understanding the application of landscape genetics methods at small spatial and temporal scales and identifying what features of the urban landscape impact urban introduced species on Oahu.We collected approximately 100 individuals of each species, sampled primarily from a 10 x10 km area in urban Honolulu, and across the larger island. Using reduced representation sequencing and landscape genetic tools, we identified roads as barriers to gene flow for two of the three species, and urban land use and very dry to seasonally mesic climates as conducive to gene flow in both A. sagrei and P. laticauda. All three species had low genetic differentiation across the island, and limited evidence of isolation by distance in Honolulu, which accords with the fact that they are recent introductions. Genetic patterns and relationships were not the same across the three species, nor between Honolulu and Oahu. Our data shows weak support for human mediated jump dispersal at an island-wide scale, and diffusive dispersal at a city-wide scale, but we suspect these patterns are obscured by the lack of time since introduction. The analysis provides insights into the genetics of urban introduced species on Oahu, how they interact with their urban environment, and into the timescales with which landscape genetic patterns emerge across an urban landscape.
The relationship between group size and population abundance in foraging birds and ungulates
(University of Hawai'i at Manoa, 2023) Rouhbakhsh, Aubtin; Ferguson, Jake M.; Wright, Amber N.; Zoology
Group foraging is a commonly observed phenomenon across various taxa that has been shown to improve an individual's fitness. There are tradeoffs to foraging in groups, with benefits such as reducing predation risk and costs such as increased competition within and between groups. The combination of these factors determines the optimal group size. While these factors are known to be density dependent, group size itself has not been explicitly tested for density dependence. Here I use an ODE model to show that the optimal group size in a population can exhibit density dependence. My model predicts that the optimal group size displays a power-law relationship with abundance, with a coefficient that depends on how predators respond to changes in their prey abundance. I then tested this model using existing empirical data and found that results were consistent across both the empirical and theoretical results. Previous work has shown that power-law group formation can stabilize predator-prey dynamics. Here I identify the key driving factors behind this pattern of group formation. My work contributes to a growing body of work that groups, rather than individuals, play a primary role in the population dynamics of group-forming fauna. This also illustrates how an individual's behavior, namely the decision to join a group, can scale up to be a significant driver of population dynamics in birds and ungulates.
Phylogenomics of ʻēkaha kū moana: insights for future biodiversity assessments
(University of Hawai'i at Manoa, 2023) Shizuru, Leah Elizabeth Kamilipua; Toonen, Robert J.; Zoology
Phylogenomics revolutionizes our understanding of evolutionary relationships among organisms by harnessing extensive genomic data. This approach provides unparalleled insights into evolutionary history by leveraging large-scale genomic data from multiple genes or entire genomes, arguably surpassing the limitations of single-gene studies. Phylogenomics offers enhanced accuracy and resolution, accounting for diverse genetic changes like mutations, insertions, deletions, and structural variations across genomes, ensuring robust evolutionary reconstructions. This method enables the elucidation of complex evolutionary patterns, estimation of species divergence times, and illumination of evolutionary processes such as adaptation and selection pressures. Moreover, phylogenomic studies are pivotal in informing conservation policies by delineating genetic relationships and evolutionary histories guiding efforts to understand biodiversity, genetic diversity, and adaptive potential. This thesis employed phylogenomic methods to assess the evolutionary relationships among antipatharians (black corals), specifically black corals (in Hawaiian ʻēkaha kū moana) collected across the Hawaiian Archipelago. The first thesis chapter details the discovery of the first mitogenome from Cirrhipathes (Cirrhipathes cf. anguina LS-2022), collected in Kauaʻi, Hawaiʻi, while the second chapter presents complete mitochondrial genomes from ten individuals across six antipatharian species (Antipathes grandis, Antipathes griggi, Aphanipathes verticillata, Cirrhipathes cf. anguina, Myriopathes cf. ulex and Stichopathes sp.) sampled from the Main and Northwestern Hawaiian Islands. These investigations provide critical insights into the evolutionary framework of ʻēkaha kū moana in the Hawaiian Archipelago, contributing substantially to our understanding of their genetic diversity.
Mosquito-associated bacterial communities source from diet and environmental substrates
(University of Hawai'i at Manoa, 2023) Weber, Danya; Medeiros, Matthew C I; Zoology
Symbiotic microorganisms are often critical for metazoan host biological functioning. Over life stages, hosts acquire symbionts from their environment, though the specific environmental sources of microbial symbionts in hosts remain largely understudied. Moreover, patterns of microbial community assembly from these environmental sources are inadequately described. Here, we utilize two mosquito species of public health and conservation concern in Hawaiʻi to test the hypothesis that host microbiomes are composed of subsets of microbes from a high diversity microbial community in the environment, and that hosts acquire these microbial symbionts through their diet. We also experimentally test the effects of the microbial environment and diet on mosquito microbiome assembly. Our field results demonstrate nestedness of mosquito symbionts within the microbial community of the mosquito diet and free-living environmental substrates. We observed partitioning of microbiome composition by host status, in which microbiome compositions are more similar between plant and animal hosts in contrast to free-living environmental substrates. Additionally, our laboratory experiment showed the re-establishment of several naturally-occurring symbiont taxa in lab-reared mosquitoes with exposure to microbial-rich natural substrates, as well as significant interaction effects of microbial source pools from larval rearing environment and adult nutritional resources on microbiome composition. Our results have implications toward understanding the microbial community assemblage and environmental sources of symbionts, which can not only answer fundamental questions related to the diversity of the host microbiome, but can also help to inform mosquito management to augment human health and conservation efforts.
Using single nucleotide polymorphisms to resolve the population structure and origins of deepwater Etelis snappers in the North Pacific Ocean
(University of Hawaii at Manoa, 2022) Lee, Anne M.; Bowen, Brian R.; Zoology
Deepwater Etelis snappers economically and culturally support fisheries in Hawai’i and throughout the Indo-Pacific. In Hawai’i, Etelis coruscans (“onaga”) and Etelis carbunculus (“ehu”) are the most abundantly harvested in the Deep 7 Bottomfish Complex, therefore it is important to understand genetic connectivity to make proper management implementations. In addition, understanding their origins will provide further information on how to ensure sustainable stocks within Hawai’i waters. Previous studies have shown that Johnston Atoll is the gateway for marine species to colonize the Hawaiian Archipelago. An alternative route is that marine species can colonize from the west, essentially Japan. To resolve population structure and the origin of the Hawaiian cohorts, we used single nucleotide polymorphisms (SNPs) to assess E. coruscans (N = 59) and E. carbunculus (N = 55), sampled from Japan, Johnston Atoll (nearest habitat south of Hawai’i), the Main Hawaiian Islands (MHI), and the Northwestern Hawaiian Islands (NWHI). Johnston Atoll samples were excluded from E. carbunculus. For both species, Japan was significantly differentiated with pairwise FST values for MHI and NWHI, and there was non-significant FST values between MHI and NWHI. Etelis coruscans showed no significant FST values between Johnston and MHI/NWHI. STRUCTURE plot of Etelis coruscans showed no genetic clustering, indicating larval exchange from both locations, Japan and Johnston Atoll. STRUCTURE plot of E. carbunculus showed clear population distinction between Japan and Hawaiian Islands, therefore we can tentatively suggest larval exchange between Johnston Atoll and Hawaiian population. To explore this idea further, future studies should focus sampling effort on Johnston to accurately make this suggestion. Management implications and strategies are needed to ensure long term sustainability of these populations of deepwater Etelis snappers. The indeterminate origin of the Hawaiian population may indicate that gene genealogies (i.e. phylogeography) are more appropriate than allele frequencies (SNPs) in resolving colonization routes.
Insights from foraging behavior on competitive interactions in introduced lizards in Hawai‘i
(University of Hawaii at Manoa, 2022) Carranza, Jose Angel; Wright, Amber N.; Zoology
Foraging behaviors have different effects on multiple aspects of an animal’s ecology. The fitness of an animal depends heavily on the body condition of said animal, and foraging has a direct effect on body condition. Foraging behaviors also dictate the types of prey predatory animals hunt, and where they hunt for this prey, both of which can drive competition for food. Exploitation competition could be a mechanism of competition being driven by foraging behaviors. Using focal animal sampling, we compared different aspects of foraging behavior on three species of invasive diurnal lizards in Hawai’i that may be competing for food: Anolis sagrei, Anolis carolinensis, and Phelsuma laticauda. Lizards were housed in single-species populations in experimental enclosures with similar prey and habitat availability. We observed differences in the heights at which Anolis sagrei and Phelsuma laticauda would forage, and Anolis carolinensis overlapped with both species. Anolis sagrei and Anolis carolinensis used the ground to forage, whereas Phelsuma laticauda was rarely seen using the ground to forage and used smooth substrates more than the other two species. Both Anolis species had similar long distances traveled to a prey item, whereas Phelsuma laticauda rarely traveled long distances to attempt to capture prey. There was overlap between all three species in the prey taxa they would hunt, which is supported by other work done on Anolis. Because of overlap in foraging behavior seen among the species, exploitation competition could be occurring and help explain why Anolis carolinensis has declined in abundance on O’ahu since the introduction of the other two species.
Life History Differences Along The Fast-slow Continuum In Introduced Lizards In Hawai‘i
(University of Hawaii at Manoa, 2022) Alascio, Spencer D.; Wright, Amber N.; Zoology
A species’ life history is the set of traits related to the timing and nature of events related to growth, reproduction, and survival. Life history strategies often occur along a ‘fast’ vs. ‘slow’ continuum, and fast life histories are frequently associated with invasion success. We documented life history traits in introduced brown anole (Anolis sagrei), green anole (Anolis carolinensis) and gold dust day gecko (Phelsuma laticauda) lizards to determine whether species differences along the fast-slow axis can help explain community changes on Oʻahu, Hawaiʻi over time. Single species populations were established in replicate 10m x10m seminatural enclosures and censused weekly for one year to track growth and survival of colonists and their offspring. We fit capture-mark-recapture models and logistic-by-weight growth models to estimate population size, survival rate, and time to sexual maturity. We documented a tradeoff between growth and survival, two key life history traits on the fast slow continuum. Brown anole females reached sexual maturity twice as fast as female green anoles and almost three times as fast as female day geckos, while male brown anoles had the lowest monthly survival probability compared to all other groups. Brown anole population estimates showed rapid population increase and high densities, and day geckos reached similar population abundance to brown anoles by the end of the study. Conversely, green anoles decreased in population size and abundance remained lower than the other species throughout the study. All three species had comparable total biomass estimates over time despite variation in abundance, suggesting an upper limit on lizard biomass set by resource availability in enclosures. The high abundance of brown anoles and day geckos, coupled with the low population abundance of green anoles, despite being on relatively opposite ends of the fast slow continuum, mirrors observed population dynamics on O‘ahu where green anoles have become rarer following the introduction and spread of the other two species. These results suggest that relatively extreme life history strategies may be favored in this environment.
The Visual Opsin And Phototransduction Pathway Genes Associated With Eye Reduction And Loss In Bat Flies (Streblidae, Nycteribiidae)
(University of Hawaii at Manoa, 2021) Atkins, Melissa Leigh; Porter, Megan L.; Zoology
Evolutionary reduction of visual sensing ability is common in troglobiont species where no light filters into the habitat. Independent of light environments, parasitism is also well-known to be associated with a reduction in eye structures. The combination of these two ecological features is exhibited in the aptly named bat fly, a parasitic arthropod that feeds on bat hosts, many of which are cave-roosting. In line with other parasitic arthropods, bat flies exhibit rudimentary development of their visual system. They are derived from fully visual, free-living ancestors, but the varying degrees of eye reduction observed throughout the clade make them a unique group of species to study. Although both parasitic and troglobitic species are well-known to be associated with a reduction in eye structures, the extent of gene loss and transcription attenuations that are accompanied with eye-loss are not well-studied. In insect compound eyes, visual perception is dependent on the number of ommatidia present and how light is focused onto the underlying receptors. Thus far, studies of bat fly macro-morphology from different species have described eyes containing from 0 to 57 facets. This diverse macro-morphology is thought to reflect microstructural changes associated with low light levels such as rhabdomere rearrangement of photoreceptor cells. In order to investigate changes in the molecular components associated with these anatomical changes, I assembled de novo transcriptomes from eight bat fly species and de novo genomes from seven bat fly species. These 15 samples represent a taxonomically diverse set of species with facet numbers ranging 0 to 12. All assemblies were annotated for opsin genes, which encode proteins that are responsible for light detection. Thus far, our analyses of genomes reveal that a common dipteran rhodopsin, Rh1, is present in all bat fly species, with an additional rhodopsin, Rh6, present in Cyclopodia dubia, though Rh1 was the only opsin to have expression at the transcriptome level. Multi-level analyses using both transcriptomes and genomes allows for confirmation of sequences and a more comprehensive understanding of the RNA transcript expression levels in reduced eyes. This work aims to elucidate the evolutionary trajectories of broader ectoparasite and troglobiont trends in visual system reductions through the absence of rhodopsin paralogs and phototransduction cascade genes.
A taxonomic study of the Spionidae (Annelida: Polychaeta) from the Hawaiian Islands and Johnston Atoll with notes on their ecology and biogeographical distribution
(University of Hawaii at Manoa, 1981) Ward, Linda Ann; Zoology
Examination of polychaetous annelids collected from the intertidal and subtidal waters of the Hawaiian Islands and Johnston Atoll between 1975 and 1980 has led to the identification of 30 species of Spionidae which are described here. Twenty-four of the 3
Aspects of the biology and ecology of Cypraea moneta at Eniwetok Atoll, Marshall Islands
(University of Hawaii at Manoa, 1971) Renaud, Maurice L.; Zoology
This thesis is a study which provides a description of certain aspects of the life history, behavior, breeding and ecology of Cypraea moneta. It was stimulated by the observation of the presence of two distinct shell types among the money cowries, Cyprae
Age, growth, reproduction and diet of Myripristis amaena at Johnston Atoll
(University of Hawaii at Manoa, 1986) Dee, Anderson James; Zoological Sciences
The M. amaena population at Johnston Atoll (JA) was used for this study. Although nothing unique has been observed about this population, JA seems an appropriate place to study M. amaena for several reasons. It is plentiful and easily collected at many lo
Recruitment And Symbiont Interactions In Anthropogenically Altered Habitats: The Porifera Of Maunalua Bay, Oʻahu
(University of Hawaii at Manoa, 2020) Wallstrom, Michael Allen; Reed, Floyd A.; Zoology
Marine ecosystems around the world are affected by anthropogenically-induced disturbances, impacting the competition for benthic space by sessile invertebrates. To investigate the recruitment of Porifera in Maunalua Bay, Oʻahu, Hawaiʻi, Porifera abundances were compared to two earlier studies, Coles et al. (2002) and Longenecker et al. (2011), to understand changes through time. Cyanobacterial symbiont interactions were tested by determining chlorophyll concentration in the sponge holobiont. There has been a significant increase in Porifera since 2011 and Porifera are now more prevalent in areas where the invasive alga, Gracilaria salicornia, is dominant compared to nearby native sea grass beds. Recruitment of Porifera to the invasive algal mats was not explained by resource partitioning facilitated by cyanobacterial symbionts. Over time and through successional regimes, endemic, native, and non-native Porifera have become established in invasive algal mats and the new niche space that they provide.
An In-depth Investigation Of Resource Fishes Within And Surrounding A Community-based Subsistence Fishing Area At Hāʻena, Kauaʻi
(University of Hawaii at Manoa, 2019) Weible, Rebecca Marie; Hunter, Cynthia L.; Zoology
Nearshore fisheries in Hawaiʻi have been steadily decreasing for over a century. Marine Protected Areas (MPAs) have been proposed as a method to both conserve biodiversity and enhance fisheries. I compared biomass and abundance of fisheries resource species inside and outside a recently established MPA on the north shore of the island of Kaua‘i. The Hāʻena Community Based Subsistence Fishing Area (CBSFA) employs a unique adaptive management strategy from which rules and regulations were established in 2015. In situ visual surveys of fishes, invertebrates, and benthos were conducted using a stratified random sampling design to evaluate the efficacy of the MPA, beginning in 2016. L50 values—defined as the size at which half of the individuals in a population have reached reproductive maturity—were used as proxies for identifying reproductively mature resource fishes both inside and outside the CBSFA. Surveys between 2016 and 2018 revealed significantly higher resource fish biomass outside the CBSFA boundaries, at deeper sites both within and outside the boundaries, as well as in pavement habitats compared with other habitat types. Although several species had higher biomass and abundances within the CBSFA boundaries, there was no strong evidence for a reserve effect at this time.
Reproduction and genetic parentage in a pair-living hermaphrodite, the intertidal limpet Siphonaria gigas
(University of Hawaii at Manoa, 2019) Schaefer, Jessica Lynn Binder; Marko, Peter B.; Zoology
Pair-living is a common social system found across animal taxa, and the relationship between pair-living and reproduction varies greatly among species. Siphonaria gigas, a hermaphroditic pulmonate gastropod, often live in pairs in the rocky intertidal. Combining genetic parentage analysis using four polymorphic microsatellite loci with behavioral observations from a 10-week field study, I provide the first description of the mating system of a Siphonaria species incorporating genetic data. S. gigas mated both within-pair and extra-pair and three out of four paired S. gigas individuals produced egg masses with extra-pair paternity. Multiple paternity was detected, but at a relatively low frequency (19% of egg masses) compared to other marine gastropods. Behavioral data indicate one potential advantage of pair-living: paired S. gigas produced almost twice as many egg masses as their solitary counterparts over four reproductive cycles. These observations, together with constraints on the movement of S. gigas, suggest that pairing may be a strategy to ensure mate access.
Indirect and Direct Effects of Competitor Presence on Behavior of Introduced Anoles in Hawai‘i
(University of Hawaii at Manoa, 2019) Kennedy-Gold, Stevie Rose; Wright, Amber N.; Zoology
The intensity and frequency of aggressive behaviors are often used as evidence for interference competition. Much like the non-consumptive effects of predators on prey, competitor presence and/or costly aggressive interactions could have indirect effects on competitor behavior. Although phenomena consistent with competition between Anolis carolinensis and Anolis sagrei have been well documented, the mechanism driving the interaction is largely unknown and little work has examined the direct and indirect effects of competitor presence when these species co-occur. Using focal animal sampling, we compared time budgets of each species when housed in experimental mesocosms containing either one or both species. Interspecific aggression was not observed, suggesting that aggressive interference is not a mechanism driving competition. However, individuals of both species when in the presence of their competitor behaved differently compared to individuals in the absence of their competitor. Alterations in time spent engaged particularly in foraging and display behaviors could explain changes in population sizes and habitat use when these species co-occur and also suggests that multiple mechanisms, as opposed to just interference or exploitation, may be driving competition between A. sagrei and A. carolinensis.
Veronicella Cubensis And Laevicaulis Alte, Invasive Slugs In The Hawiian Islands: Life Histories And The Gut Microbiome
(University of Hawaii at Manoa, 2018-12) Sommer, Rachel Mary; Cowie, Robert; Zoology
Veronicella cubensis and Laevicaulis alte are widespread invasive slugs. Although they are voracious pests and known carriers of Angiostrongylus cantonensis, little is understood of the characters that make them successful invaders. To gain a more comprehensive understanding of these species, a study of their life histories was conducted. Slugs were reared in a lab setting to gather data on lifespan reproductive trends. The effect of temperature on juvenile growth was also determined by tracking the weight gain of slugs maintained in either a hot or cool temperature environment over the first six months of life. Observations of the egg laying behavior of V. cubensis prompted analysis of the gut microbiome and the possibility of transmission of the microbiome from parent to offspring from a substance laid on its egg masses. Veronicella cubensis reaches reproductive maturity at around 6 months of age and exhibits long duration mating and egg laying. The egg masses of both species contain a variable number of eggs, which hatch with a high success rate. Warmer temperatures cause faster weight gain in V. cubensis juveniles but not in those of L. alte. Microbiome analyses suggest the substance laid on V. cubensis egg masses comes from the adult slug hindgut, and the bacterial community on the surface of the eggs constitutes a component of the bacteria acquired by juveniles. These results are a valuable addition to the limited knowledge of the reproductive biology of these veronicellid species; they will help us to understand why they are such successful invaders and thereby to predict and prevent their further spread.
The Effects of Habitat Specialization on Population Structure in Hawaiian Damselfies
(University of Hawaii at Manoa, 2017-12) Henry, Elizabeth R.; Zoology
Hawaiʻi is a diverse ecological hotspot of biodiversity, home to many adaptive radiations including a clade of damselflies which encompass the full known range of damselfly breeding habitats and encompass a range of habitat specificity but are of increasing conservation concern. I tested the effects that habitat specificity might have on gene flow and population differentiation between a relative generalist Megalagrion vagabundum and a relative specialist Megalagrion nigrohamatum nigrolineatum. Mitochondrial genes indicate that there is significant differentiation at a fine-scale in M. vagabundum and suggests that differentiation may be even stronger in M. n. nigrolineatum. These data are further discussed with respect to genetic variation within these two species and possible barriers to dispersal and the ecology and conservation of these two Megalagrion species.
The Effects of Oxygen Supply when Immersed on the Thermal Limits and Performance of the Wave Zone Echinoderm Colobocentrotus atratus
(University of Hawaii at Manoa, 2017-08) Wilbur, Sean L.; Zoology
Thermal limits of marine ectotherms are hypothesized to be limited by oxygen demand. This limit arises from an animal’s metabolic demand outpacing oxygen supply and delivery with increasing temperatures. We applied this theory to the intertidal zone, where animals are exposed to extreme temperature ranges and emersion, to examine how oxygen delivery capacity can limit vertical distributions of organisms. We tested the upper thermal limit of performance (survival and attachment strength) in a wave-zone obligate urchin, Colobocentrotus atratus, under both ambient (21%) and enriched (35%) O2 conditions, to determine if these urchins are limited by oxygen availability in water when exposed to temperatures ranging from 25 to 37⁰C. Survival when thermally stressed was increased by enriched O2 conditions, indicating oxygen limitation of C. atratus under submerged conditions. Attachment strength declined with increasing temperature, but was not affected by O2 enrichment. Our data support that the lower limit on vertical distributions of C. atratus are set by abiotic conditions resulting from oxygen limitation when submerged.
Detecting Bias in Phylogenetic Inference: Empirical Tests of Posterior Predictive Model Assessment
(University of Hawaii at Manoa, 2016-05) Richards, Emilie
Inferring the ‘Tree of Life’ depends heavily on statistical models of sequence evolution. As is the case with all statistical inference, these models are only approximations of the actual evolutionary processes they are meant to describe. When a model poorly describes a given dataset, the resulting phylogeny can be inaccurate. Methods that directly assess goodness of fit are increasingly being recognized as the means to circumvent this problem, although this framework is still in its infancy within phylogenetics. Here we use phylogenies inferred from several hundred mitochondrial genomes to assess the performance of these new approaches at detecting poor absolute model fit and related problems. This study provides clear examples of when these new methods prove useful. We also detect some unforeseen behaviors for larger, more complex datasets where these methods are most critically needed. These issues point the way forward for future development of this emerging framework in phylogenetics.

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