Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago

Aim

The biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (Sus verrucosus) and Bawean (S. blouchi) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation.

Location

Malay Archipelago, with focus on Bawean and Java.

Methods

We employed genome-wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times and to perform demographic model selection.

Results

In contrast to the hypothesis of recent divergence during the last glacial maximum, S. blouchi was found to have diverged from S. verrucosus at least 166 k years ago following a founder event. The contemporary S. blouchi population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of S. blouchi, as was previously proposed based on morphometrics. The demographic history of S. verrucosus showed evidence of secondary contact with the sympatric banded pig (S. scrofa vittatus) that colonised Java 70 k years ago.

Main Conclusions

While the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both S. verrucosus and S. blouchi. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation.     

Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

Background  

It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood.     

Ancient geographical gaps and paleo-climate shape the phylogeography of an endemic bird in the sky islands of southern India

Background

Sky islands, formed by the highest reaches of mountain tracts physically isolated from one another, represent one of the biodiversity-rich regions of the world. Comparative studies of geographically isolated populations on such islands can provide valuable insights into the biogeography and evolution of species on these islands. The Western Ghats mountains of southern India form a sky island system, where the relationship between the island structure and the evolution of its species remains virtually unknown despite a few population genetic studies.

Methods and Principal Findings

We investigated how ancient geographic gaps and glacial cycles have partitioned genetic variation in modern populations of a threatened endemic bird, the White-bellied Shortwing Brachypteryx major, across the montane Shola forests on these islands and also inferred its evolutionary history. We used Bayesian and maximum likelihood-based phylogenetic and population-genetic analyses on data from three mitochondrial markers and one nuclear marker (totally 2594 bp) obtained from 33 White-bellied Shortwing individuals across five islands. Genetic differentiation between populations of the species correlated with the locations of deep valleys in the Western Ghats but not with geographical distance between these populations. All populations revealed demographic histories consistent with population founding and expansion during the Last Glacial Maximum. Given the level of genetic differentiation north and south of the Palghat Gap, we suggest that these populations be considered two different taxonomic species.

Conclusions and Significance

Our results show that the physiography and paleo-climate of this region historically resulted in multiple glacial refugia that may have subsequently driven the evolutionary history and current population structure of this bird. The first avian genetic study from this biodiversity hotspot, our results provide insights into processes that may have impacted the speciation and evolution of the endemic fauna of this region.     

Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)

Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype‐by‐sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.     

On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

Background  

Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale). We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations.     

Investigations of fine-scale phylogeography in Tigriopus californicus reveal historical patterns of population divergence

Background  

The intertidal copepod Tigriopus californicus is a model for studying the process of genetic divergence in allopatry and for probing the nature of genetic changes that lead to reproductive isolation. Although previous studies have revealed a pattern of remarkably high levels of genetic divergence between the populations of this species at several spatial scales, it is not clear what types of historical processes are responsible. Particularly lacking are data that can yield insights into population history from the finest scales of geographic resolution.     

Genetic diversity and colony structure of Tapinoma melanocephalum on the islands and mainland of South China

Aim

Tapinoma melanocephalum is listed as one of the most important invasive pest species in China. Information regarding the patterns of invasion and effects of geographic isolation on the population genetics of this species is largely lacking.

Location

South China.

Methods

To address this problem, we genotyped 39 colonies (two colonies were collapsed due to genetic similarity) using microsatellite markers and mitochondrial DNA sequencing to compare colony genetic structure of T. melanocephalum on the mainland and islands of South China.

Results

An analysis of the colony genotypes showed that the genetic diversity of the mainland population was slightly higher than that of the island populations but not significantly so. However, the observed heterozygosity on Shangchuan Island (SCD) was significantly lower than that of the other colonies. We also found six haplotypes in 111 mitochondrial DNA COI sequences. The relatedness (r) value between colonies of SCD was 0.410, higher than that of the other populations. The genetic clusters among colonies were not related to geographic locations and exhibited admixture likely due to frequent human‐mediated dispersal associated with trade between the mainland population and the islands. Pairwise F_STs between populations showed differentiation among mainland populations, while SCD displayed high levels of divergence (F_ST > 0.15) from most mainland populations. There was no significant isolation by distance among colonies. Most populations showed signs of a bottleneck effect.

Main conclusions

Our study suggests that there was no significant difference in the genetic diversity among the islands and the mainland; however, the lower genetic diversity, the higher degree of genetic divergence from other colonies, and the higher relatedness among nestmates made the SCD population stand out from all the others.     

Rapid ecological isolation and intermediate genetic divergence in lacustrine cyclic parthenogens

Background  

Ecological shifts can promote rapid divergence and speciation. However, the role of ecological speciation in animals that reproduce predominantly asexually with periodic sex and strong dispersal, such as lacustrine cladocerans, is poorly understood. These life history traits may slow or prevent ecological lineage formation among populations. Proponents of the postglacial ecological isolation hypothesis for Daphnia suggest that some species have formed postglacially in adjacent, but ecologically different habitats. We tested this hypothesis with ecological, morphological, and multilocus coalescence analyses in the putative lacustrine sister species, Daphnia parvula and Daphnia retrocurva.     

The identity,distribution, and impacts of non-native apple snails in the continental United States

Background  

Since the mid 1990s populations of non-native apple snails (Ampullariidae) have been discovered with increasing frequency in the continental United States. Given the dramatic effects that introduced apple snails have had on both natural habitats and agricultural areas in Southeast Asia, their introduction to the mainland U.S. is cause for concern. We combine phylogenetic analyses of mtDNA sequences with examination of introduced populations and museum collections to clarify the identities, introduced distributions, geographical origins, and introduction histories of apple snails.     

Pleistocene glacial cycle effects on the phylogeography of the Chinese endemic bat species, <Emphasis Type="Italic">Myotis davidii</Emphasis>

Background  

Global climatic oscillations, glaciation cycles and the unique geographic topology of China have profoundly influenced species population distributions. In most species, contemporary distributions of populations cannot be fully understood, except in a historical context. Complex patterns of Pleistocene glaciations, as well as other physiographic changes have influenced the distribution of bat species in China. Until this study, there had been no phylogeographical research on Myotis davidii, an endemic Chinese bat. We used a combination of nuclear and mitochondrial DNA markers to investigate genetic diversity, population structure, and the demographic history of M. davidii. In particular, we compared patterns of genetic variation to glacial oscillations, topography, and environmental variation during the Pleistocene in an effort to explain current distributions in light of these historical processes.     

Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes? – Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity

Background  

Circum-Antarctic waters harbour a rare example of a marine species flock – the Notothenioid fish, most species of which are restricted to the continental shelf. It remains an open question as to how they survived Pleistocene climatic fluctuations characterised by repeated advances of continental glaciers as far as the shelf break that probably resulted in a loss of habitat for benthic organisms. Pelagic ecosystems, on the other hand, might have flourished during glacial maxima due to the northward expansion of Antarctic polar waters. In order to better understand the role of ecological traits in Quaternary climatic fluctuations, we performed demographic analyses of populations of four fish species from the tribe Trematominae, including both fully benthic and pelagic species using the mitochondrial cytochrome b gene and an intron from the nuclear S7 gene.     

Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N_e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma. The inferred ancestral N_e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10^?9) or third glaciation (mutation rate = 9 × 10^?9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.     

Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence

Background  

Introduced species can have profound effects on native species, communities, and ecosystems, and have caused extinctions or declines in native species globally. We examined the evolutionary response of native zooplankton populations to the introduction of non-native salmonids in alpine lakes in the Sierra Nevada of California, USA. We compared morphological and life-history traits in populations of Daphnia with a known history of introduced salmonids and populations that have no history of salmonid introductions.     

Long- term effects of previous experience determine nutrient discrimination abilities in birds

Background

The evolution of reproductive traits, such as hybrid incompatibility (postzygotic isolation) and species recognition (prezygotic isolation), have shown their key role in speciation. Theoretical modeling has recently predicted that close linkage between genes controlling pre- and postzygotic reproductive isolation could accelerate the conditions for speciation. Postzygotic isolation could develop during the sympatric speciation process contributing to the divergence of populations. Using hybrid fitness as a measure of postzygotic reproductive isolation, we empirically studied population divergence in perch (Perca fluviatilis L.) from two genetically divergent populations within a lake.

Results

During spawning time of perch we artificially created parental offspring and F₁ hybrids of the two populations and studied fertilization rate and hatching success under laboratory conditions. The combined fitness measure (product of fertilization rate and hatching success) of F₁ hybrids was significantly reduced compared to offspring from within population crosses.

Conclusion

Our results suggest intrinsic genetic incompatibility between the two populations and indicate that population divergence between two populations of perch inhabiting the same lake may indeed be promoted by postzygotic isolation.     

Rapid evolution in response to introduced predators II: the contribution of adaptive plasticity

Background  

Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined phenotypic and genetic responses of Daphnia populations to recent introductions of non-native fish to assess the relative roles of phenotypic plasticity versus genetic change in causing the observed patterns. The Daphnia community in alpine lakes throughout the Sierra Nevada of California (USA) is ideally suited for investigation of rapid adaptive evolution because there are multiple lakes with and without introduced fish predators. We conducted common-garden experiments involving presence or absence of chemical cues produced by fish and measured morphological and life-history traits in Daphnia melanica populations collected from lakes with contrasting fish stocking histories. The experiment allowed us to assess the degree of population differentiation due to fish predation and examine the contribution of adaptive plasticity in the response to predator introduction.     

Comparative phylogeography of two related plant species with overlapping ranges in Europe, and the potential effects of climate change on their intraspecific genetic diversity

Background  

The aim of the present study was to use a combined phylogeographic and species distribution modelling approach to compare the glacial histories of two plant species with overlapping distributions, Orthilia secunda (one-sided wintergreen) and Monotropa hypopitys (yellow bird's nest). Phylogeographic analysis was carried out to determine the distribution of genetic variation across the range of each species and to test whether both correspond to the "classic" model of high diversity in the south, with decreasing diversity at higher latitudes, or whether the cold-adapted O. secunda might retain more genetic variation in northern populations. In addition, projected species distributions based on a future climate scenario were modelled to assess how changes in the species ranges might impact on total intraspecific diversity in both cases.     

‘On being the right size’ – Do aliens follow the rules?

Aim

To assess whether mammalian species introduced onto islands across the globe have evolved to exhibit body size patterns consistent with the ‘island rule,’, and to test an ecological explanation for body size evolution of insular mammals.

Location

Islands worldwide.

Methods

We assembled data on body mass, geographical characteristics (latitude, maximum elevation) and ecological communities (number of mammalian competitors, predators and prey) for 385 introduced populations across 285 islands, comprising 56 species of extant, non‐volant mammals. We used linear regression, ANCOVA and regression tree analyses to test whether introduced populations of mammals exhibit the island rule pattern, whether the degree of body size change increased with time in isolation and whether residual variation about the general trend can be attributed to the geographical and ecological characteristics of the islands.

Results

Introduced populations follow the predicted island rule trend, with body size shifts more pronounced for populations with greater residence times on the islands. Small mammals evolved to larger body sizes in lower latitudes and on islands with limited topographic relief. Consistent with our hypothesis on the ecology of evolution, body size of insular introduced populations was influenced by co‐occurring species of mammalian competitors, predators and prey.

Conclusion

The island rule is a pervasive pattern, exhibited across a broad span of geographical regions, taxa, time periods and, as evidenced here, for introduced as well as native mammals. Time in isolation impacts body size evolution profoundly. Body size shift of introduced mammals was much more pronounced with increasing residence times, yet far less than that exhibited by native, palaeo‐insular mammals (residence times > 10,000 years). Given the antiquity of many species introductions, it appears that much of what we view as the natural character and ecological dynamics of recent insular communities may have been rendered artefacts of ancient colonizations by humans and commensals.     

Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis)

Background  

Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica.     

Unveiling an ancient biological invasion: molecular analysis of an old European alien, the crested porcupine (Hystrix cristata)

Background  

Biological invasions can be considered one of the main threats to biodiversity, and the recognition of common ecological and evolutionary features among invaders can help developing a predictive framework to control further invasions. In particular, the analysis of successful invasive species and of their autochthonous source populations by means of genetic, phylogeographic and demographic tools can provide novel insights into the study of biological invasion patterns. Today, long-term dynamics of biological invasions are still poorly understood and need further investigations. Moreover, distribution and molecular data on native populations could contribute to the recognition of common evolutionary features of successful aliens.     

Risk of extinction increases towards higher elevations across the world's amphibians

Aim

Life in mountains is associated with multiple features that increase the risk of demographic collapses in populations – small geographic ranges, short breeding seasons, specialization to harsh climates – leading to the hypothesis that extinction risk is exacerbated in species inhabiting higher elevations. Here, we implement the first test of this hypothesis across the amphibian tree of life – the tetrapods with the largest proportion of montane species, and nature's most threatened animals.

Location

Global.

Time Period

Present.

Major Taxa Studied

Class Amphibia.

Methods

We collated a dataset spanning 8042 species from across all three amphibian orders (Anura, Caudata and Gymnophiona). We preformed phylogenetic logistic regressions to test the predictions that extinction risk increases with elevation, and whether this effect is caused by factors previously hypothesised to drive high-elevation declines, including restrictions on species' geographic ranges, variation in their life histories and the presence of infectious disease.

Results

Globally, extinction risk increases towards higher elevations. At order-level, this relationship holds for frogs and salamanders. Even when controlling for geographic range size, life histories and infectious disease, extinction risk increases with elevation for amphibians combined and frogs globally, and in the Americas. In contrast, whereas extinction risk is greater among high-elevation Eurasian amphibians, this relationship is explained by larger body sizes and lower fecundity.

Main Conclusions

Our analyses indicate that after considering factors previously thought to explain the increase in extinction risk towards higher elevations (e.g., geographic range size, disease), elevation remains a significant predictor of amphibian extinction risk. Given that the only available tests of this hypothesis in other tetrapods (birds and reptiles) conflict with our findings, we suggest that physiological or life-history features of amphibians may explain this observed phenomenon.