Species Delimitation and Diversification History in Rhinoceros Beetles: How Many and Why So Many Species?

I address two grand challenges in biology – species delimitation and speciation process. Additionally, I attempt to bridge the gap between macro- and micro-evolutionary studies. The characteristics of two groups of rhinoceros beetles (genus Dynastes and Xylotrupes) make them ideal for addressing these questions – geographically widespread taxa with local morphological forms – also make them challenging to study. These groups exhibit inconsistency in taxonomic designations and their geographic distributions imply complex historical processes in their diversification process. My research highlights both the power, but also the necessity, of an integrative framework that considers different data types, as well as quantitative approaches to test different hypotheses about species boundaries and the diversification process. For example, my first chapter revealed the arbitrariness in taxonomic decisions, even between closely related taxa from the same lineage, by demonstrating that species boundaries were statistically equivalent among taxa even though some were assigned as subspecies. By establishing this taxonomic foundation, my studies on the effects of ecological and geographic isolation on species diversification in the following chapters avoid the biases introduced by taxonomic ambiguity and inconsistency. In my second chapter, I show that the effects of habitat stability/instability outweighs the contributions of geological events that connect previously isolated biotas in promoting rapid diversification in Hercules beetles. Following the general theme of the contribution of different barriers to divergence, in Chapter 3 I test whether their effects are similar across different levels of biological organization – that is, in the structuring of patterns of genetic diversity among population, species, and faunal communities. This work shows that oceanic barriers between landmasses in the Indo-Australian Archipelago delineates zoological regions by structuring distinct faunal communities and promotes population subdivision in Xylotrupes beetles. However, the rate of species diversification is associated with shifts in forest fragmentation across geological times. As such, this work highlights the decoupling of processes contributing to micro- and macroevolutionary patterns, which only became evident because of my integrative approach that involves consideration of alternative mechanisms and study of divergence at multiple levels of biodiversity.PhDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133411/1/huangjp_1.pd

The great American biotic interchange and diversification history in Dynastes beetles (Scarabaeidae; Dynastinae)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134267/1/zoj12393.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134267/2/zoj12393_am.pd

Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes, Dynastinae)

The prevalence and consequences of genetic introgression between species have been intensively debated. I used Hercules beetles as examples to test for conditions that may be associated with the occurrence of introgression. RADseq data were used to reconstruct the species tree and history of introgression between Hercules beetles. Image data from museum specimens were used to investigate the phenotypic similarity of two adaptive traits between species from two distinct climatic realms (Nearctic vs. Neotropical). Genetic introgression was identified between Hercules beetles living in geographic proximity (parapatric). Phylogenetic relatedness and phenotypic similarity did not predict nor preclude genetic introgression between species. Phenotypic assimilation in body coloration was evident between distantly related Hercules beetles codistributed in Central America, where directional introgression was also statistically supported from the putative donor to receiver lineages. The number of introgressed loci was significantly higher between species with than without phenotypic similarity. I discuss the implications of recent studies on adaptive genetic introgression by providing supporting evidence from the Hercules beetle system.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134423/1/mec13849_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134423/2/mec13849.pd

Lineage-specific late pleistocene expansion of an endemic subtropical gossamer-wing damselfly, Euphaea formosa, in Taiwan

Abstract Background Pleistocene glacial oscillations have significantly affected the historical population dynamics of temperate taxa. However, the general effects of recent climatic changes on the evolutionary history and genetic structure of extant subtropical species remain poorly understood. In the present study, phylogeographic and historical demographic analyses based on mitochondrial and nuclear DNA sequences were used. The aim was to investigate whether Pleistocene climatic cycles, paleo-drainages or mountain vicariance of Taiwan shaped the evolutionary diversification of a subtropical gossamer-wing damselfly, Euphaea formosa. Results E. formosa populations originated in the middle Pleistocene period (0.3 Mya) and consisted of two evolutionarily independent lineages. It is likely that they derived from the Pleistocene paleo-drainages of northern and southern Minjiang, or alternatively by divergence within Taiwan. The ancestral North-central lineage colonized northwestern Taiwan first and maintained a slowly growing population throughout much of the early to middle Pleistocene period. The ancestral widespread lineage reached central-southern Taiwan and experienced a spatial and demographic expansion into eastern Taiwan. This expansion began approximately 30,000 years ago in the Holocene interglacial period. The ancestral southern expansion into eastern Taiwan indicates that the central mountain range (CMR) formed a barrier to east-west expansion. However, E. formosa populations in the three major biogeographic regions (East, South, and North-Central) exhibit no significant genetic partitions, suggesting that river drainages and mountains did not form strong geographical barriers against gene flow among extant populations. Conclusions The present study implies that the antiquity of E. formosa's colonization is associated with its high dispersal ability and larval tolerance to the late Pleistocene dry grasslands. The effect of late Pleistocene climatic changes on the subtropical damselfly's historical demography is lineage-specific, depending predominantly on its colonization history and geography. It is proposed that the Riss and Würm glaciations in the late Pleistocene period had a greater impact on the evolutionary diversification of subtropical insular species than the last glacial maximum (LGM).http://deepblue.lib.umich.edu/bitstream/2027.42/112629/1/12862_2010_Article_1702.pd

The Hercules beetles (subgenus Dynastes, genus Dynastes, Dynastidae): a revisionary study based on the integration of molecular, morphological, ecological, and geographic analyses

The taxonomic treatment of Hercules beetles (subgenus Dynastes of the genus Dynastes MacLeay, 1819) is revised, with the recognition of two major species groups and 15 species. The following 10 taxa, originally designated as subspecies, have been elevated to full species status: Dynastes moroni Nagai, 2005 (REVISED STATUS); Dynastes bleuzeni Silvestre and Dechambre, 1995 (NEW STATUS); Dynastes ecuatorianus Ohaus, 1913 (NEW STATUS); Dynastes lichyi Lachaume, 1985 (NEW STATUS); Dynastes morishimai Nagai, 2002 (NEW STATUS); Dynastes occidentalis Lachaume, 1985 (NEW STATUS); Dynastes paschoali Grossi and Arnaud, 1993 (NEW STATUS); Dynastes reidi Chalumeau, 1977 (NEW STATUS); Dynastes septentrionalis Lachaume, 1985 (NEW STATUS); and Dynastes trinidadensis Chalumeau and Reid, 1995 (NEW STATUS). The use of the species name Dynastes hercules (Linnaeus, 1758) is restricted to only two island populations from Guadeloupe and Dominica. This taxonomic revision is accompanied by discussions of the basis for these taxonomic changes, i.e. based on differences in genetic, phenotypic, and ecological data and on estimates of geographic overlap. An updated Dynastes beetle phylogeny based on Illumina sequencing data is also presented for a discussion of the evolutionary relationships among the species.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138820/1/MP206.pdfDescription of MP206.pdf : Main articl

Polychlorinated biphenyls, dichlorodiphenyldichloroethylene, and infant development and growth: an analysis of the PIN Babies Study

Polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT) are persistent, bioaccumulative and toxic pollutants which were broadly used in the US until the 1970s. Common exposure to PCBs, DDT, and dichlorodiphenyldichloroethylene (DDE), the most stable metabolite of DDT, may influence children's neurodevelopment and growth, but study results are not consistent. This dissertation reported the concentrations of PCBs, DDT and DDE in breast milk of lactating women in Central North Carolina in 2004-2006, and examined the associations between lactational exposure to PCBs, DDT and DDE and infant development and growth at 12 months using data from the Pregnancy, Infection and Nutrition Babies Study, 2004-2006. PCBs, DDT and DDE were measured in breast milk at the third month postpartum. Lactational exposure of these chemicals was estimated by the product of chemical concentrations and the duration of breast feeding. Infant development at 12 months was measured by the Mullen Scales of Early Learning (n=231) and the Short Form: Level I (infant) of the MacArthur-Bates Communicative Development Indices (CDI) (n=218). Serial infant growth measurements through the first 12 months of life were regularly recorded in each child's growth card by pediatric practitioners (n=206). No consistent associations were observed between lactational exposure to PCBs, DDT and DDE through the first 12 months and the measures of infant development. However, DDE was associated with scoring below average on the gross motor scale of the Mullen among males only (adjusted OR=1.9, 95%CI=1.1, 3.3). Among infants breast fed for 6 months or longer there was no difference in weight and length through the first 6 months as the concentrations of PCBs, DDT and DDE increased. No difference was observed in weight and length at 12 months when comparing the accumulated lactational exposure through 12 months after controlling for total duration of breast feeding. In the ranges of chemical concentrations studied here, combined with the beneficial effects of the long duration of breastfeeding in this study population, lactational exposure to PCBs, DDT and DDE did not appear to impair infant neurodevelopment at 12 months, and resulted in no negative influence on infant growth in the first 12 months

Effects of gap size, temperature and pumping pressure on the fluid dynamics and chemical kinetics of in-line spatial atomic layer deposition of Al2O3

Abstract: Low throughput is a major limitation for industrial level atomic layer deposition (ALD) applications. Spatial ALD is regarded as a promising solution to this issue. With numerical simulations, this paper studies an in-line spatial ALD reactor by investigating the effects of gap size, temperature, and pumping pressure on the flow and surface chemical deposition processes in Al2O3 ALD. The precursor intermixing is a critical issue in spatial ALD system design, and it is highly dependent on the flow and material distributions. By numerical studies, it’s found that bigger gap, e.g., 2 mm, results in less precursor intermixing, but generates slightly lower saturated deposition rate. Wafer temperature is shown as a significant factor in both flow and surface deposition processes. Higher temperature accelerates the diffusive mass transport, which largely contributes to the precursor intermixing. On the other hand, higher temperature increases film deposition rate. Well-maintained pumping pressure is beneficial to decrease the precursor intermixing level, but its effect on the chemical process is shown very weak. It is revealed that the time scale of in-line spatial ALD cycle is only in tens of milliseconds, i.e., ~15 ms. Considering that the in-line spatial ALD is a continuous process without purging step, the ALD cycle time is greatly shortened, and hence the overall throughput is shown as high as ~8 nm/s, compared to several nm/min in traditional ALD

Upper Water Structure and Mixed Layer Depth in Tropical Waters: The SEATS Station in the Northern South China Sea

The variability of the upper water hydrographic structure, the efficacy of the different schemes for estimating the mixed layer depth (MLD), the inter-comparability estimation of the MLDs and diurnal and intra-annual MLD climatology in the tropical waters in the northern South China Sea were accessed in 702 depth-profiles of potential temperature (θ) and salinity collected in 64 cruises between 17.5 and 18.5°N and 115.3 and 116.3°E from 1997 to 2013. The hydrographic structure may be subdivided into three principal types: the classical type, with quasi-isopycnal surface mixed layer followed by an abrupt increase in the depth-gradient in θ and potential density (σθ) to mark the MLD; the stepwise type, with one or more small stepwise decreases in θ and/or increases in σθ in the mixed layer; and the graded type, with a general decrease in θ and increases in σθ with depth into the main pycnocline without a clear break to mark the MLD. These three types of upper waters were found in 75, 10, and 15% of the cruises. Out. of the 10 schemes for estimating the MLD, only the fixed temperature difference method of 0.5 and 0.8°C from the 10-m temperature yielded consistent results, with root mean square error and mean absolute percentage difference of 2 m and 2%. MLD varied diurnally with an average standard deviation of 4 m from the mean. The monthly average MLD reached a maximum of 80 m in December/January and dropped to a minimum of 25 m in May