Kent Holsinger

• Ph.D. in Biological Sciences
• Professor at University of Connecticut

The prediction accuracy of estimated breeding values using traditional best linear unbiased prediction (PBLUP) and single-step genomic BLUP (ssGBLUP) methods was investigated in two breeding populations of Litopenaeus vannamei, using simulated data with varying levels of marker density. Additionally, the impact of the number of generations with phe...

Variation in plant traits related to size and architecture, water relations, and resource uptake reflect important dimensions of plant function that may explain how different species are adapted to their local environments. Within a local community, variation in many of these traits may promote coexistence of competing species through niche partiti...

Premise: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function. Methods: We examined the distribution of g...

PREMISE The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function. METHODS We examined the distribution of genet...

Conserving biodiversity in an era of rapid climate change requires understanding the mechanisms that influence dispersal, gene flow and, ultimately, species persistence. This information is becoming critical for conserving key species in rapidly warming places such as the Arctic. Arctic freshwater fish not only face warmer conditions, but also the...

Climate change is affecting species composition and diversity across the globe. Phenological changes provide a sensitive indicator of biological responses to changes in climate. Recent studies using herbarium records in Europe and North America have shown changes in flowering time and other phenological events in response to changing climate condit...

Background and aims: Global plant trait datasets commonly identify trait relationships that are interpreted to reflect fundamental trade-offs associated with plant strategies, but often these trait relationships are not identified when evaluating them at smaller taxonomic and spatial scales. In this study we evaluate trait relationships measured o...

Premise of the study: Plant traits are often associated with the environments in which they occur, but these associations often differ across spatial and phylogenetic scales. Here we study the relationship between microenvironment, microgeographical location, and traits within populations using co-occurring populations of two closely related everg...

Evolutionary radiations are responsible for much of Earth's diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as “adaptive” or not. Across many groups o...

Protea punctata and P. venusta are closely related, but morphologically distinct, species that naturally hybridize in the wild. Here we examined patterns of hybridization and cryptic introgression in seedlings grown from seeds collected at Blesberg Mountain in the Swartberg Mountain range. We used restriction site associated genotyping by sequencin...

PREMISE OF THE STUDY: American bipolar plant distributions characterize taxa at various taxonomic ranks but are most common in the bryophytes at infraspecific and infrageneric levels. A previous study on the bipolar disjunction in the dung moss genus Tetraplodon found that direct long-distance dispersal from North to South in the Miocene–Pleistocen...

Better understanding and prediction of tree growth is important because of the many ecosystem services provided by forests and the uncertainty surrounding how forests will respond to anthropogenic climate change. With the ultimate goal of improving models of forest dynamics, here we construct a statistical model that combines complementary data sou...

Better understanding and prediction of tree growth is important because of the many ecosystem services provided by forests and the uncertainty surrounding how forests will respond to anthropogenic climate change. With the ultimate goal of improving models of forest dynamics, here we construct a statistical model that combines complementary data sou...

Premise of the study: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the...

Premise of the study: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogen...

Understanding the environmental and genetic mechanisms underlying locally adaptive trait variation across the ranges of species is a major focus of evolutionary biology. Combining transcriptome sequencing with common garden experiments on populations spanning geographical and environmental gradients holds promise for identifying such mechanisms. Th...

Background and aims: Trait-environment relationships are commonly interpreted as evidence for local adaptation in plants. However, even when selection analyses support this interpretation, the mechanisms underlying differential benefits are often unknown. This study addresses this gap in knowledge using the broadly distributed South African shrub...

Polymorphic traits are central to many fundamental discoveries in evolution, yet why they are found in some species and not others remains poorly understood. We use the African genus Protea-within which more than 40% of species have co-occurring pink and white floral colour morphs-to ask whether convergent evolution and ecological similarity could...

Evolutionary radiations with extreme levels of diversity present a unique opportunity to study the role of the environment in plant evolution. If environmental adaptation played an important role in such radiations, we expect to find associations between functional traits and key climatic variables. Similar trait-environment associations across cla...

Protea mundii Klotsch (Proteaceae) has a disjunct distribution, with a large range in the Eastern Cape between Knysna and Port Elizabeth, and a smaller one in the Western Cape between Betty's Bay and Hermanus. Here, we provide population genetic and morphological evidence that populations in the two ranges belong to two distinct evolutionary lineag...

Premise of research.Evolutionary radiations can be driven by physiological tolerances. Protea is a species-rich genus in the Cape Floristic Region of South Africa and provides the opportunity to examine whether drought response traits may have contributed to differentiation in this stress-tolerant genus. Commonly utilized drought responses might be...

Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized...

Understanding the mechanisms that allow biological species to co-occur is of great interest to ecologists. Here we investigate the factors that influence co-occurrence of members of the genus Protea in the Cape Floristic Region of southwestern Africa, a global hot spot of biodiversity. Due to the binomial nature of our response, a critical issue is...

Local adaptation along steep environmental gradients likely contributes to plant diversity in the Cape Region of South Africa, yet existing analyses of trait divergence are limited to static measurements of functional traits rather than trajectories of individual development. We explore whether five taxa of evergreen shrubs (Protea section Exsertae...

The coexistence of different color morphs is often attributed to variable selection pressures across space, time, morph frequencies, or selection agents, but the routes by which each morph is favored are rarely identified. In this study we investigated factors that influence floral color polymorphisms on a local scale in Protea, within which approx...

Background/Question/Methods Plant and animal species face many threats to survival including land use changes, disruption of mutualisms, and climate change. However, some species face further complications from human harvest. We focused on the harvest of the Malagasy orchid, Erasanthe henrici, which is collected for the horticultural market. This...

Remote sensing data can represent various habitat characteristics, and thus can substitute for detailed ground sampling when constructing habitat models. To predict saltmarsh sparrow (Ammodramus caudacutus) distribution and nesting activity, we compared Bayesian hierarchical models in which variables were generated from field or remote sensing data...

Over the past 40 years, an increasing number of previously unrecorded populations of a colonial ascidian, recently identified as Didemnum vexillum, have been documented in most temperate coastal regions of the world, impacting aquaculture operations, natural rocky habitats, cobble/gravel substrates, and eelgrass beds. The earliest sample thought to...

The many documented examples of parallel and convergent evolution in similar environments are strong evidence for the role of natural selection in the evolution of trait variation. However, species may respond to selection in different ways; idiosyncrasies of their evolutionary history may affect how different species respond to the same selective...

We examined habitat factors related to reach-scale brook trout Salvelinus fontinalis counts of four size classes in two headwater stream networks within two contrasting summers in Connecticut, USA. Two study stream networks (7.7 and 4.4 km) were surveyed in a spatially continuous manner in their entirety, and a set of Bayesian generalised linear mi...

Covariation between vital rates is recognized as an important pattern to be accounted for in demographic modeling. We recently introduced a model for estimating vital rates and their covariation as a function of known and unknown effects, using generalized linear mixed models (GLMM's) implemented in a hierarchical Bayesian framework (Evans et al.,...

The text of a funded proposal in the National Science Foundation's Dimensions of Biodiversity program. PIs are Carl Schlichting, Cindi Jones, Carl Schlichting, and Kent Holsinger (University of Connecticut); Andrew Latimer (University of California - Davis); and Justin Borevitz. Funded in September 2010.

A funded (summer 2007) proposal to the National Science Foundation for analysis of one evolutionary radiation within the genus Protea.

Notes that accompany a lecture on reserve design when I taught a graduate level course in conservation biology. These notes provide an introductory overview to the theory and design of nature reserves.

Background/Question/Methods Phenotypic plasticity may be an important contributor to the success of many invasive plant species. Shifts in genotype induced by the recipient environment can also lead to a range of phenotypic expression not seen in the native range. Selection for these novel genotypes could lead to local adaptation in the introduce...

Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying m...

Competing evolutionary forces shape plant breeding systems (e.g. inbreeding depression, reproductive assurance). Which of these forces prevails in a given population or species is predicted to depend upon such factors as life history, ecological conditions, and geographical context. Here, we examined two such predictions: that self-compatibility sh...

The principle of parsimony is a useful methodological tool in the choice between competing hypotheses if the hypotheses are of equal explanatory power. Its use is defended by the discussion of several examples, and a recent objection to its use is shown to be the result of a misinterpretation of the principle.

The US Botanical Capacity Assessment Project (BCAP) was initiated as a first step to gauge the nation's collective ability to meet the environmental challenges of the 21st century. The project, in which the authors of this article are involved, specifically aimed to identify multisector contributions to and gaps in botanical capacity in order to de...

Plant population growth and persistence are strongly influenced by germination and recruitment, which can be dramatically affected by seed dormancy, local site conditions, seed size and seed predation. Understanding factors that limit germination can help to explain low recruitment rates and is particularly important for species of conservation con...

Local adaptation along environmental gradients may drive plant species radiation within the Cape Floristic Region (CFR), yet few studies examine the role of ecologically based divergent selection within CFR clades. In this study, we ask whether populations within the monophyletic white protea clade (Protea section Exsertae, Proteaceae) differ in ke...

Understanding and predicting changes in the abundance of natural populations is a central goal of ecology. These changes are influenced by a variety of exogenous processes (weather, floods, fire); variation in these processes leads to variation in vital rates (survival, fecundity) that may be positively or negatively correlated across the life cycl...

Increased nitrogen (N) deposition, resulting from the combustion of fossil fuels, production of synthetic fertilizers, growth of N(2)-fixing crops and high-intensity agriculture, is one of the anthropogenic factors most likely to cause global biodiversity changes over the next century. This influence may be especially large in temperate zone forest...

An important fraction of recently generated molecular data is dominant markers. They contain substantial information about genetic variation but dominance makes it impossible to apply standard techniques to calculate measures of genetic differentiation, such as F-statistics. In this article, we propose a new Bayesian beta-mixture model that more ac...

Adaptive radiations likely underlie much of the world's diversity, especially that of hyper-diverse regions. They are usually characterized by a burst of speciation early in their evolutionary history, a pattern which can be detected using population genetic tools. The Cape Floristic Region (CFR) of southwestern South Africa is home to many spectac...

Unlabelled: Premise of the study: The processes maintaining flower color polymorphisms have long been of evolutionary interest. Mechanistic explanations include selection through pollinators, antagonists, local environments, drift, and pleiotropic effects. We examined the maintenance of inflorescence color polymorphisms in the genus Protea (Prot...

Unlabelled: Premise of the study: We examined two accounts of the relationship between breeding system and life history variation in a clade of evening primroses (Oenothera, Onagraceae): (1) selection for reproductive assurance should generate an association between self-compatibility and monocarpy and (2) phylogenetic conservatism leads to rete...

Wright's F-statistics, and especially F(ST), provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of F(ST) can identify regions of the genome that hav...

Background/Question/Methods Understanding and predicting fluctuations in the abundance of natural populations is a central activity of ecology. Natural populations are inevitably under the influence of stochastic processes (weather, floods, fire); this environmental variation causes variation in vital rates (survival, fecundity) which may be positi...

We investigated the role of an ornamental, purple-leaved specimen of Japanese barberry in a local invasion using parentage analysis. We focused on a landscape plant of B. thunbergii var. atropurpurea in Willington, CT, that was first established at least 30 years ago. We genotyped every barberry plant found within a 92-m radius of this individual....

The distribution of genetic variation among populations is conveniently measured by Wright's F(ST), which is a scaled variance taking on values in [0,1]. For certain types of genetic markers, and for single-nucleotide polymorphisms (SNPs) in particular, it is reasonable to presume that allelic differences at most loci are selectively neutral. For s...

We used parentage analysis to estimate seedling recruitment distances and genetic composition of seedling patches centred around reproductive trees of the animal-dispersed Neotropical canopy palm Iriartea deltoidea in two 0.5 ha plots within second-growth forest and one 0.5 ha plot in adjacent old-growth forest at La Selva Biological Field Station...

The distribution of genetic variation among populations is conveniently measured by Wright’s FST , which is a scaled variance taking on values in [0,1]. For certain types of genetic markers, and for single-nucleotide polymorphisms (SNPs) in particular, it is reasonable to presume that allelic differences at most loci are selectively neutral. For su...

We propose a hierarchical Bayesian model to estimate the proportional contribution of source populations to a newly founded colony. Samples are derived from the first generation offspring in the colony, but mating may occur preferentially among migrants from the same source population. Genotypes of the newly founded colony and source populations ar...

Japanese barberry (Berberis thunbergii DC.) is a widespread invasive plant that remains an important landscape shrub represented by ornamental, purple-leaved forms of the botanical variety atropurpurea. These forms differ greatly in appearance from feral plants, bringing into question whether they contribute to invasive populations or whether the i...

Managing populations, either for conservation, harvesting, or control, requires a mechanistic or semi-mechanistic understanding of population dynamics. Here, we investigate how time-since-fire affects demographic transitions in an endangered plant, Dicerandra frutescens ssp. frutescens (Lamiaceae), which is specialized to gaps created by fire. We u...

Iriartea deltoidea (Arecaceae) is an abundant canopy palm with a wide geographic distribution in Neotropical wet forests. We analyzed the genetic profile across three generations of Iriartea within a 43-ha area encompassing two areas of second-growth and adjoining old-growth forest at La Selva Biological Field Station in northeastern Costa Rica. A...

Urtica dioica ("stinging nettle") includes both dioecious and monoecious forms. In most sexually dimorphic angiosperm species, the genetic mechanisms of sex determination are completely unknown. The few species that include both monoecious and dioecious forms provide an unusual opportunity to examine the genetic mechanisms that underlie the separat...

This paper presents a methodology for model fitting and inference in the context of Bayesian models of the type f(Y | X,θ)f(X|θ)f(θ), where Y is the (set of) observed data, θ is a set of model parameters and X is an unobserved (latent) stationary stochastic process induced by the first order transition model f(X (t+1)|X (t),θ), where X (t) denotes...

The fundamental data of population genetics consists of allele counts at different loci within populations. The natural descriptive statistics associated with these data are locus specific allele frequencies and measures to describe the partitioning of genetic diversity within and among populations. F-statistics, which were first introduced by Sewa...

In January, 2005 Lawrence Summers, President of Harvard University, ignited a firestorm when he suggested that the small number of women on science faculties reflects intrinsic differences in the distribution of scientific aptitude between men and women. While he may have been wrong about those differences, men and women are different in many ways...

Populations may become differentiated from one another as a result of genetic drift. The amounts and patterns of differentiation at neutral loci are determined by local population sizes, migration rates among populations, and mutation rates. We provide exact analytical expressions for the mean, variance, and covariance of a stochastic model for hie...

Lecture notes from my graduate course in population genetics. Topics covered include basic principles of Hardy-Weinberg, population structure, drift, mutation, selection, quantitatitve genetics, molecular evolution, and phylogeography. Please contact me if you find errors or places where the explanations are unclear or incomplete. The first link be...

There is substantial evidence that environmental changes on a landscape level can have dramatic consequences for the species richness and structure of food webs as well as on trophic interactions within such food webs. Thus far, the consequences of environmental change, and particularly the effects of invasive species and the fragmentation and isol...

Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch leng...

Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of popul...

Secondary forests are more extensive than old-growth forests in many tropical regions, yet the genetic composition of colonizing populations is poorly understood. We analyzed the parentage of a founder population of 130 individuals of the canopy palm Iriartea deltoidea in a 24-year-old second-growth forest in lowland Costa Rica. Among 66 trees in a...

Aim Determine the phylogeny and dispersal patterns of the cicada genus Kikihia in New Zealand and the origin of the Norfolk, Kermadec, and Chatham Island cicadas. Location New Zealand, Norfolk Island, Kermadec Islands and Chatham Island. Methods DNA sequences from 16 species and four soon to be described species of cicadas from New Zealand and Norf...

We present a framework for fitting multiple random walks to animal movement paths consisting of ordered sets of step lengths and turning angles. Each step and turn is assigned to one of a number of random walks, each characteristic of a different behavioral state. Behavioral state assignments may be inferred purely from movement data or may include...

We tested for genetic variation in light response curves and their acclimation to sun versus shade in recombinant inbred lines (RILs) of the annual species Impatiens capensis derived from a cross between sun and shade populations. We exposed replicates of 49 RILs to experimentally manipulated light levels (open versus shade) in a greenhouse and mea...

Bayesian approaches have been widely applied to partitioning diversity within and among levels in many different multi-level modeling contexts. In spite of the structural similarities between these Bayesian models and hierarchical approaches to partitioning diversity in population genetics, population geneticists have not explored the use of hierar...

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Informatio...

Aim Determine the geographical and temporal origins of New Zealand cicadas. Location New Zealand, eastern Australia and New Caledonia. Methods DNA sequences from 14 species of cicadas from New Zealand, Australia, and New Caledonia were examined. A total of 4628 bp were analysed from whole genome extraction of four mitochondrial genes (cytochrome ox...

The size advantage hypothesis suggests that natural selection will favor size-dependent sex expression when one sex gains more than the other by being large. But members of a minority sex will also have a higher reproductive value, on average. Thus, an individual's reproductive success depends on the reproductive decisions made by neighboring indiv...