Xia Hua

Australian National University | ANU · Department of Mathematics

Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing f...

How long does speciation take? The answer to this important question in evolutionary biology lies in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently...

Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, corr...

Exchange in ideas between language evolution and biological evolution has a long history, due to a shared theoretical foundation between language and biology as two evolving systems. Both systems evolve in terms of the frequency of a variant in a population for each of a large number of variables, that is how often a particular variant of a languag...

Macroevolutionary analysis is increasingly being used to study biodiversity responses to climate change, for example by using phylogenetic node ages to infer periods of diversification, or phylogenetic reconstruction of traits to infer adaptation to particular stresses. Here we apply a recently developed macroevolutionary method to investigate the...

Language diversity is under threat. While each language is subject to specific social, demographic and political pressures, there may also be common threatening processes. We use an analysis of 6,511 spoken languages with 51 predictor variables spanning aspects of population, documentation, legal recognition, education policy, socioeconomic indicat...

Temperature differences over time and space has been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning...

Linguistic coherence—the co-variation of language variants within speaker repertoires— has been proposed as a key process driving the divergence of language dialects. Previous studies on coherence have been often limited by dataset sizes and analyses. We analyze the use of 185 variables across 78 speakers from the Gurindji community in Australia. W...

Spicier food in hot countries has been explained in terms of natural selection on human cultures, with spices with antimicrobial effects considered to be an adaptation to increased risk of foodborne infection. However, correlations between culture and environment are difficult to interpret, because many cultural traits are inherited together from s...

How long does speciation take? What are the speciation processes that generated a species group? The answers to these important questions in evolutionary biology lie in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to...

Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing f...

Aim Macroevolutionary analysis is increasingly being used to study biodiversity responses to climate change, for example by using phylogenetic node ages to infer periods of diversification, or phylogenetic reconstruction of traits to infer adaptation to particular stresses. Here we apply a recently developed macroevolutionary method to investigate...

Aim Phylogenetic diversity or phylo‐diversity measures use information about evolutionary history and relationships to inform conservation priorities. These metrics are usually derived from the branches of molecular phylogenies. But inferring phylogenetic timescale from molecular data relies on many assumptions about the evolutionary process, most...

A central theme connecting macroevolutionary processes to macroecological patterns is the shaping of regional biodiversity over time through speciation, extinction, migration and range shifts. The use of phylogenies to explore the dynamics of diversification due to variation in speciation and extinction rates has been well‐developed and there are e...

Environmental stress response in plants has been studied using a wide range of approaches, from lab‐based investigation of biochemistry and genetics, to glasshouse studies of physiology and growth rates, to field‐based trials and ecological surveys. It is also possible to investigate evolution of environmental stress responses using macroevolutiona...

Although parasites are known to have various effects on their hosts, we know little about their role in the assembly of diversifying host populations. Using an experimental bacterium (Pseudomonas fluorescens SBW25)-bacteriophage (ϕ2) system, we show that earlier parasite arrival significantly reduced the repeatability of host diversification. Earli...

The world is facing a crisis of language loss that rivals, or exceeds, the rate of loss of biodiversity. There is an increasing urgency to understand the drivers of language change in order to try and stem the catastrophic rate of language loss globally and to improve language vitality. Here we present a unique case study of language shift in an en...

The ecological niche of species is often studied from two different perspectives. Environmental niche modelling (ENM) infers a species’ current niche from contemporary occurrence records, while phylogenetic comparative methods (PCM) infer the history of niche evolution. Although these two areas of research are conceptually linked, they are analysed...

Language diversity is distributed unevenly over the globe. Intriguingly, patterns of language diversity resemble biodiversity patterns, leading to suggestions that similar mechanisms may underlie both linguistic and biological diversification. Here we present the first global analysis of language diversity that compares the relative importance of t...

We report on the rapid birth of a new language in Australia, Gurindji Kriol, from the admixture of Gurindji and Kriol. This study is the first investigation of contact-induced change within a single speaker population which uses multiple variants. It also represents an innovative modification of the Wright-Fisher population genetics model to invest...

Language diversity is distributed unevenly over the globe. Why do some areas have so many different languages and other areas so few? Intriguingly, patterns of language diversity resemble biodiversity patterns, leading to suggestions that similar mechanisms may underlie both linguistic and biological diversification. Here we present the first globa...

A growing number of studies seek to identify predictors of broad-scale patterns in human cultural diversity, but three sources of non-independence in human cultural variables can bias the results of cross-cultural studies. First, related cultures tend to have many traits in common, regardless of whether those traits are functionally linked. Second,...

What role does speaker population size play in shaping rates of language evolution? There has been little consensus on the expected relationship between rates and patterns of language change and speaker population size, with some predicting faster rates of change in smaller populations, and others expecting greater change in larger populations. The...

Non-random species sampling is the rule rather than the exception in phylogenetics, but most phylogenetic methods to infer macroevolutionary and macroecological processes assume that the tips of the phylogenetic tree are either completely sampled or randomly sampled. In this study, we focus on extending the popular BiSSE framework to better account...

Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a 'molecular clock'. Although ini...

Significance Do different aspects of language evolve in different ways? Here, we infer the rates of change in lexical and grammatical data from 81 languages of the Pacific. We show that, in general, grammatical features tend to change faster and have higher amounts of conflicting signal than basic vocabulary. We suggest that subsystems of language...

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in...

A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an u...

Being invoked as one of the candidate mechanisms for the latitudinal patterns in biodiversity, Janzen’s hypothesis states that the limited seasonal temperature variation in the tropics generates greater temperature stratification across elevations, which makes tropical species adapted to narrower ranges of temperatures and have lower effective disp...

Bayesian phylogenetic analyses estimate posterior distributions of phylogenetic tree topologies and other parameters using Markov chain Monte Carlo (MCMC) methods. Before making inferences from these distributions, it is important to assess their adequacy. To this end, the Effective Sample Size (ESS) of a parameter estimates how many truly independ...

Interdisciplinary research is widely considered a hothouse for innovation, and the only plausible approach to complex problems such as climate change. One barrier to interdisciplinary research is the widespread perception that interdisciplinary projects are less likely to be funded than those with a narrower focus. However, this commonly held belie...

Specialization has often been claimed to be an evolutionary dead end, with specialist lineages having a reduced capacity to persist or diversify. In a phylogenetic comparative framework, an evolutionary dead end may be detectable from the phylogenetic distribution of specialists, if specialists rarely give rise to large, diverse clades. Previous ph...

Patterns of trait distribution on phylogenies bear the imprint of the macroevolutionary mechanisms that have shaped them. Phylogenetic metrics can be used to summarize these patterns and potentially could be used to uncover the macroevolutionary mechanisms. However, their utility has been limited by the difficulty in constructing proper null distri...

Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focussed on "positive" lineage selection, where stably heritable properties of li...

The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: that the rate of mitochondrial mutations is negatively correlated with longevit...

Background Salt tolerance in plants is rare, yet it is found across a diverse set of taxonomic groups. This suggests that, although salt tolerance often involves a set of complex traits, it has evolved many times independently in different angiosperm lineages. However, the pattern of evolution of salt tolerance can vary dramatically between familie...

A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of ang...

Significance Evolutionary methods are increasingly being applied to investigating linguistic change. But does language change conform to the predictions of evolutionary theory? Here, we use data from closely related pairs of languages to show that a key prediction of evolutionary theory is met: rates of gain of new words are higher in larger popula...

Salt tolerance has evolved many times independently in different plant groups. One possible explanation for this pattern is that it builds upon a general suite of stress-tolerance traits. If this is the case, then we might expect a correlation between salt tolerance and other tolerances to different environmental stresses. This association has been...

The factors that set species range limits underlie many patterns in ecology, evolution, biogeography and conservation. These factors have been the subject of several reviews, but there has been no systematic review of the causes of warm-edge limits (low elevations and latitudes). Understanding these causes is urgent, given that the factors that set...

Abstract Variation in climatic conditions over space and time is thought to be an important driver of speciation. However, the role of climate has not been explored in the theoretical literature on speciation, and the theory underlying empirical studies of climate and speciation has come largely from informal, verbal models. In this study, we devel...

Anthropogenic climate change is predicted to be a major cause of species extinctions in the next 100 years. But what will actually cause these extinctions? For example, will it be limited physiological tolerance to high temperatures, changing biotic interactions or other factors? Here, we systematically review the proximate causes of climate-change...

The treefrogs (Hylidae) make up one of the most species-rich families of amphibians. With 885 species currently described, they contain >13% of all amphibian species. In recent years, there has been considerable progress in resolving hylid phylogeny. However, the most comprehensive phylogeny to date (Wiens et al., 2006) included only 292 species, w...

Speciation often has a strong geographical and environmental component, but the ecological factors that potentially underlie allopatric and parapatric speciation remain understudied. Two ecological mechanisms by which speciation may occur on geographic scales are allopatric speciation through niche conservatism and parapatric or allopatric speciati...

The treefrog genus Hyla (Anura: Hylidae) consists of at least 31 species found in North America, Central America, Europe, and Asia and is the only genus of hylids that occurs outside the New World. Despite intensive work on the phylogeny of the genus in the past few years, several problems still exist regarding relationships within Hyla. These prob...

This study extended the geographic coverage of a previous study to explore population genetic structure and demographic history in the Ariake icefish Salanx ariakensis from three populations of continental coastlines and one island population in the north-western Pacific based on a partial sequence of the mitochondrial cytochrome b gene. The S. ari...

Aim  We studied elevational species richness patterns of Schizothorax fishes and identified the roles of ecological and evolutionary factors in shaping the patterns of elevational diversity.Location  The Tibetan Plateau and its adjacent regions.Methods  We assembled distribution and altitude data for all Schizothorax species using the literature. W...