Too Hot to Nest? In a Hot Summer the Tortoise Chersina angulata Can Switch From Nesting to Facultative Viviparity

In a captive colony of Chersina angulata in Cape Town, South Africa, we observed in 2015/16 retention of the last egg clutch inside the female until the hatching stage was reached, conforming to the generally accepted definition of viviparity. Retrospective climatic analysis indicates egg retention until the hatching stage co-occurred with unusually hot summer weather: the average air temperatures in December 2015 and January and February 2016 were higher than during the preceding five and the following 5 years when facultative viviparity could not be observed. Late December and January appears to be the critical period for females to either deposit their last clutch of the nesting season into a nest, or to retain the last clutch for embryonic development inside the female. Over the 28 December to 24 January period the minimum, average and maximum air temperatures in 2015–16 were about 3°C higher than in the five following years. This association of facultative viviparity with unusual summer heat suggests that hot ambient temperatures at the end of the nesting season may cue females to switch from oviposition to facultative viviparity. Compared to incubation in a nest this phenotypic plasticity of the reproductive mode—to retain during hot summers the season’s last clutch inside the female—may buffer the developing embryos from excessive heat exposure: females can thermo-regulate by moving among microhabitats whereas sun exposed shallow nests cannot escape high ground temperatures. This novel reproductive strategy has the potential to enhance the resilience of species to global warming.

Maternal investment evolves with larger body size and higher diversification rate in sharks and rays

Across vertebrates, live-bearing has evolved at least 150 times from the ancestral state of egg-laying into a diverse array of forms and degrees of prepartum maternal investment. A key question is how this diversity of reproductive modes arose and whether reproductive diversification underlies species diversification? To test these questions, we evaluate the most basal jawed vertebrates, Chondrichthyans, which have one of the greatest ranges of reproductive and ecological diversity among vertebrates. We reconstructed the sequence of reproductive mode evolution across a time-calibrated molecular phylogeny of 610 chondrichthyans. We find that egg-laying is ancestral, and that live-bearing evolved at least seven times. Matrotrophy (i.e. additional maternal contributions) evolved at least 15 times, with evidence of one reversal. In sharks, transitions to live-bearing and matrotrophy are more prevalent in larger-bodied species in the tropics. Further, the evolution of live-bearing is associated with a near-doubling of the diversification rate, but, there is only a small increase in diversification associated with the appearance of matrotrophy. The chondrichthyan diversification and radiation, particularly throughout the shallow tropical shelf seas and oceanic pelagic habitats, appears to be associated with the evolution of live-bearing and the proliferation of a wide range of maternal investment in their developing offspring.

Multiple Data Demonstrate That Bacteria Regulating Reproduction Could Be Not the Cause for the Thelytoky of Diglyphus wani (Hymenoptera: Eulophidae)

In Hymenoptera parasitoids, the reproductive mode is arrhenotoky, while a few species reproduce by thelytoky. The thelytoky of Hymenoptera parasitoids is generally genetically determined by the parasitoids themselves or induced by bacteria, including Wolbachia, Cardinium, and Rickettsia. Diglyphus wani (Hymenoptera: Eulophidae), a recently reported thelytokous species is a main parasitoid attacking agromyzid leafminers. To assess whether endosymbionts induce thelytoky in D. wani, we performed universal PCR detection and sequenced the V3-V4 region of 16S ribosomal RNA gene. In addition, bacteria were removed through high-temperature and antibiotic treatments, and the localized bacteria were detected using FISH. Based on general PCR detection, Wolbachia, Cardinium, Rickettsia, Arsenophonus, Spiroplasma, and Microsporidia were absent in laboratory and field individuals of thelytokous D. wani. Furthermore, 16S rRNA gene sequencing revealed that the dominant endosymbionts in thelytokous D. wani were not reproductive manipulators. High-temperature and antibiotic treatment for five consecutive generations cannot reverse the thelytokous pattern of D. wani, and no male offspring were produced. Moreover, no bacterial spots were found in the ovaries of D. wani. Thus, it is considered that the thelytoky of D. wani does not result in the presence of endosymbionts. This species is thus the second reported eulophid parasitoid whose thelytoky appears not to be associated with endosymbionts.

Genome Size, Cytotype Diversity and Reproductive Mode Variation of Cotoneaster integerrimus (Rosaceae) from the Balkans

Cotoneaster integerrimus represents a multiploid and facultative apomictic system of widely distributed mountain populations. We used flow cytometry to determine genome size, ploidy level, and reproduction mode variation of the Balkan populations, supplemented by analysis of nuclear microsatellites in order to address: (i) geographic distribution and variation of cytotypes among the populations; (ii) variation of reproduction mode and the frequency of sexuality; (iii) pathways of endosperm formation among the sampled polyploids and their endosperm balance requirements; (iv) genotypic diversity and geographic distribution of clonal lineages of polyploids. The prevalence of apomictic tetraploid cytotype followed by sexual diploids and extremely rare triploids was demonstrated. This prevalence of tetraploids affected the populations’ structure composed from clonal genotypes with varying proportions. The co-occurrence of diploids and tetraploids generated higher cytotype, reproductive mode, and genotypic diversity, but mixed-ploidy sites were extremely rare. The endosperm imbalance facilitates the development and the occurrence of intermediate triploids in mixed-ploidy populations, but also different tetraploid lineages elsewhere with unbalanced endosperm. All these results showed that the South European populations of C. integerrimus have higher levels of cytotype and reproductive diversity compared to the Central European ones. Therefore, the South European populations can be considered as a potential reservoir of regional and global diversity for this species.

An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures

Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.

Genetic Factors Associated with Variation in Abundance of the Invasive Yellow Crazy Ant (Anoplolepis gracilipes)

<p>A key component of successful invasion is the ability of an introduced population to reach sufficient abundance to persist, spread, and alter or dominate the recipient biological community. Genetic diversity is one of many factors that may contribute to population dynamics, but has important ramifications for biological fitness, and thus invasion success in the long term. I explored genetic factors associated with variation in abundance (i.e., differential invasion success) of the yellow crazy ant Anoplolepis gracilipes in the Indo-Pacific region, primarily focussing on Arnhem Land in Australia's Northern Territory. I explored five aspects that I hypothesised could contribute to variation in the abundance of this ant: 1) I investigated the unusual reproductive mode of A. gracilipes, and tested whether it involved dependent-lineage genetic caste determination (DL GCD) in Arnhem Land. In DL GCD systems populations require hybridisation between genetically distinct groups to produce both reproductive and worker castes. Asymmetry in the ratio of different lineages may result in low abundance and population collapse. I found no evidence for a DL GCD system in A. gracilipes, and thus its abundance in Arnhem Land does not appear to be constrained by any lineage ratio asymmetry. Worker reproduction (either of males or asexual production of other workers) also appeared unlikely. The reproductive mode of the species remains fascinating but enigmatic; 2) I explored whether multiple source populations were responsible for the observed variation in abundance in Arnhem Land (i.e., is abundance associated with propagule pressure, or populations from different sources), and if the population has diverged since introduction. The A. gracilipes population in Arnhem Land stemmed from a single source, and thus propagule pressure was apparently not responsible for variation in abundance. In contrast to many invasive ants, population divergence has occurred since introduction; 3) I tested the hypotheses that genetic variation was associated with variation in abundance in Arnhem Land, and that ecological success was density-dependent. While the population divergence found in Chapter 3 was not related to variation in abundance, genotypic diversity was higher in more abundant nest clusters. These more abundant nest clusters were in turn associated with lower native ant species diversity, and a difference in composition of the invaded ant community (i.e., greater ecological success); 4) I revisited the invasion of the yellow crazy ant in Tokelau to determine whether a haplotype that was linked to greater abundance and dominance of the ant community has increased in distribution. Although ants of the inferred dominant haplotype were implicated in most new invasions, their abundance was substantially lower than previously observed in Tokelau; 5) I conducted a preliminary analysis of the metagenomic diversity of A. gracilipes endogenous parasites and symbionts among populations from Christmas Island, Okinawa, Samoa and Arnhem Land. Bacterial community composition and diversity differed between the study populations. Variation in abundance among A. gracilipes populations in Arnhem Land was not due to parasite load on populations with low abundance. However, low abundance of A. gracilipes was correlated with lower microbial diversity overall, and higher prevalence of some groups, notably two that confer antibiotic properties. Together, my findings suggest that propagule pressure, reproductive mode and haplotype-specific effects do not appear to be associated with variation in A. gracilipes abundance. Other genetic factors I investigated do appear to be associated with the variation in A. gracilipes abundance and effects on the invaded ant communities. Genotypic diversity was positively related to the abundance of A. gracilipes in Arnhem Land, and this relationship may be affected by population divergence through population bottlenecks. In addition, differences in bacterial diversity among populations highlighted several candidate bacteria that could be associated with variation in abundance, which would be a topic of future work. Although genetic factors are often implicated in the successful establishment of invasive species, my thesis demonstrates that genetic factors may also be associated with post-establishment population dynamics.</p>

Genetic Factors Associated with Variation in Abundance of the Invasive Yellow Crazy Ant (Anoplolepis gracilipes)

<p>A key component of successful invasion is the ability of an introduced population to reach sufficient abundance to persist, spread, and alter or dominate the recipient biological community. Genetic diversity is one of many factors that may contribute to population dynamics, but has important ramifications for biological fitness, and thus invasion success in the long term. I explored genetic factors associated with variation in abundance (i.e., differential invasion success) of the yellow crazy ant Anoplolepis gracilipes in the Indo-Pacific region, primarily focussing on Arnhem Land in Australia's Northern Territory. I explored five aspects that I hypothesised could contribute to variation in the abundance of this ant: 1) I investigated the unusual reproductive mode of A. gracilipes, and tested whether it involved dependent-lineage genetic caste determination (DL GCD) in Arnhem Land. In DL GCD systems populations require hybridisation between genetically distinct groups to produce both reproductive and worker castes. Asymmetry in the ratio of different lineages may result in low abundance and population collapse. I found no evidence for a DL GCD system in A. gracilipes, and thus its abundance in Arnhem Land does not appear to be constrained by any lineage ratio asymmetry. Worker reproduction (either of males or asexual production of other workers) also appeared unlikely. The reproductive mode of the species remains fascinating but enigmatic; 2) I explored whether multiple source populations were responsible for the observed variation in abundance in Arnhem Land (i.e., is abundance associated with propagule pressure, or populations from different sources), and if the population has diverged since introduction. The A. gracilipes population in Arnhem Land stemmed from a single source, and thus propagule pressure was apparently not responsible for variation in abundance. In contrast to many invasive ants, population divergence has occurred since introduction; 3) I tested the hypotheses that genetic variation was associated with variation in abundance in Arnhem Land, and that ecological success was density-dependent. While the population divergence found in Chapter 3 was not related to variation in abundance, genotypic diversity was higher in more abundant nest clusters. These more abundant nest clusters were in turn associated with lower native ant species diversity, and a difference in composition of the invaded ant community (i.e., greater ecological success); 4) I revisited the invasion of the yellow crazy ant in Tokelau to determine whether a haplotype that was linked to greater abundance and dominance of the ant community has increased in distribution. Although ants of the inferred dominant haplotype were implicated in most new invasions, their abundance was substantially lower than previously observed in Tokelau; 5) I conducted a preliminary analysis of the metagenomic diversity of A. gracilipes endogenous parasites and symbionts among populations from Christmas Island, Okinawa, Samoa and Arnhem Land. Bacterial community composition and diversity differed between the study populations. Variation in abundance among A. gracilipes populations in Arnhem Land was not due to parasite load on populations with low abundance. However, low abundance of A. gracilipes was correlated with lower microbial diversity overall, and higher prevalence of some groups, notably two that confer antibiotic properties. Together, my findings suggest that propagule pressure, reproductive mode and haplotype-specific effects do not appear to be associated with variation in A. gracilipes abundance. Other genetic factors I investigated do appear to be associated with the variation in A. gracilipes abundance and effects on the invaded ant communities. Genotypic diversity was positively related to the abundance of A. gracilipes in Arnhem Land, and this relationship may be affected by population divergence through population bottlenecks. In addition, differences in bacterial diversity among populations highlighted several candidate bacteria that could be associated with variation in abundance, which would be a topic of future work. Although genetic factors are often implicated in the successful establishment of invasive species, my thesis demonstrates that genetic factors may also be associated with post-establishment population dynamics.</p>

Amphibians of the equatorial seasonally dry forests of Ecuador and Peru

Seasonally dry forests (SDFs) are one of the most challenging ecosystems for amphibians, fueling the diversity of this group of vertebrates. An updated inventory of native amphibians present in the Equatorial SDF is provided, which extends along the Pacific coast of Ecuador and northwestern Peru. The study is based on an extensive field sampling (two thirds of the total records) carried out throughout the Equatorial SDF, along with a compilation of the available information on distribution of amphibians in the region from published scientific papers, museum collections and on-line databases. The final dataset included 2,032 occurrence records for 30 amphibian species, belonging to eight anuran families. Additionally, data regarding conservation status, habitat use, spawn deposition site, reproductive mode, and body size, along with an identification key for all encountered species are provided. The results indicate a strong sampling bias with a deficit in the Peruvian part of the study area, and a need for urgent inventories targeted at under-sampled areas, using modern taxonomic methods. The study emphasizes the conservation priorities in the Equatorial SDF, based on the distribution, conservation status and life-history data. This information should be useful for the local authorities and institutions involved in the management and conservation of biodiversity in SDF.

Genetic patterns in Montipora capitata across an environmental mosaic in Kaneohe Bay

Spatial genetic structure (SGS) is important to a population's ability to adapt to environmental change. For species that reproduce both sexually and asexually, the relative contribution of each reproductive mode has important ecological and evolutionary implications because asexual reproduction can have a strong effect on SGS. Reef building corals reproduce sexually, but many species also propagate asexually under certain conditions. In order to understand SGS and the relative importance of reproductive mode across environmental gradients, we evaluated genetic relatedness in almost 600 colonies of Montipora capitata across 30 environmentally characterized sites in Kaneohe Bay, Oahu, Hawaii using low-depth restriction digest associated sequencing. Clonal colonies were relatively rare overall but influenced SGS. Clones were located significantly closer to one another spatially than average colonies and were more frequent on sites where wave energy was relatively high, suggesting a strong role of mechanical breakage in their formation. Excluding clones, we found no evidence of isolation by distance within sites or across the bay. Several environmental characteristics were significant predictors of the underlying genetic variation (including degree heating weeks, time spent above 30°C, depth, sedimentation rate and wave height); however, they only explained 5% of this genetic variation. Our results show that colony fragmentation contributes to the ecology of M. capitata at local scales and that genetic diversity is maintained despite strong environmental gradients in a highly impacted ecosystem, suggesting potential for broad adaptation or acclimatization in this population.