Disentangling the drivers of diversification in an imperiled group of freshwater fishes (Cyprinodontiformes: Goodeidae)

Geographic range size and speciation in honeyeaters

Background

Darwin and others proposed that a species’ geographic range size positively influences speciation likelihood, with the relationship potentially dependent on the mode of speciation and other contributing factors, including geographic setting and species traits. Several alternative proposals for the influence of range size on speciation rate have also been made (e.g. negative or a unimodal relationship with speciation). To examine Darwin’s proposal, we use a range of phylogenetic comparative methods, focusing on a large Australasian bird clade, the honeyeaters (Aves: Meliphagidae).

Results

We consider the influence of range size, shape, and position (latitudinal and longitudinal midpoints, island or continental species), and consider two traits known to influence range size: dispersal ability and body size. Applying several analytical approaches, including phylogenetic Bayesian path analysis, spatiophylogenetic models, and state-dependent speciation and extinction models, we find support for both the positive relationship between range size and speciation rate and the influence of mode of speciation.

Conclusions

Honeyeater speciation rate differs considerably between islands and the continental setting across the clade’s distribution, with range size contributing positively in the continental setting, while dispersal ability influences speciation regardless of setting. These outcomes support Darwin’s original proposal for a positive relationship between range size and speciation likelihood, while extending the evidence for the contribution of dispersal ability to speciation.

Differential sensitivity of offspring from four species of goodeine freshwater fish to acute exposure to nitrates

Nitrate-nitrogen (NO3-N) pollution related to anthropogenic activities is increasing in freshwater ecosystems. Knowledge about NO3-N sensitivity in freshwater wild fish is needed to understand the differential tolerance between species. Goodeinae is a subfamily of 41 endemic fishes that inhabit central Mexico, with 33 species in the IUCN red list and three extinct. Distributional patterns suggest tolerant and sensitive goodeines related to the conservation gradient of freshwater ecosystems. Four species with a differential distribution and tolerance were selected to evaluate their physiological responses to NO3-N. Fish were exposed to different NO3-N concentrations for 96 h and the median lethal concentration (LC50) was determined. Swimming disorders plus gill and liver histopathological indexes were estimated and incorporated into an Integrated Biomarker Response (IBR) for each species. Skiffia lermae (LC50 = 474.332 mg/L) and Xenotoca variata (LC50 = 520.273 mg/L) were more sensitive than Goodea atripinnis (LC50 = 953.049 mg/L) and Alloophorus robustus (LC50 = 1537.13 mg/L). The typical histological damage produced by NaNO3-N exposure was fusion of secondary lamellae in gills. This was present in all species and cellular degeneration was observed at the highest concentrations. Secondary lamellae aneurysms were only observed in G. atripinnis. Liver alterations included vascular dilation in hepatic sinusoids, hyperemia and nuclear hypertrophy; higher concentrations produced hepatocyte cytoplasmic vacuolation and reduced frequency of cell nuclei. Behavioral and histopathological alterations could explain the differential species sensitivity. The results suggest that species which preserve gill function and transfer the task of detoxification to the liver might have the best chance of surviving in polluted environments. Moreover, species previously considered as tolerant may be highly susceptible to NaNO3-N exposure. Therefore, it is necessary to closely monitor NaNO3-N concentrations in freshwater ecosystems and, if possible, reduce their levels to avoid the loss of wild populations.

Expression and antimicrobial activity of liver-expressed antimicrobial peptides in the ovaries of the viviparous teleost Xenotoca eiseni

The mechanism via which the mothers of viviparous animals regulate the internal environment of pregnancy-associated organs for maintaining offspring growth is poorly understood. Environmental niches in organs contain fluid components for supporting embryonic growth; however, they may serve as nutrients for microbes. Therefore, microbial control is essential in viviparous animals to reduce the risk of infection in the ovarian lumen. Its importance may be higher than that in the case of oviparous animals. In this study, we investigated the antimicrobial factors in a viviparous teleost, Xenotoca eiseni. Four transcripts of the liver-expressed antimicrobial peptide (LEAP) were identified via RNA-Seq analysis. Some of the genes were expressed in the ovaries or intraovarian embryos of the fish. In particular, high expression of leap1a was detected in the ovaries of both pregnant and non-pregnant fish. Moreover, the ovary extracts from X. eiseni and transformed leap genes exhibited antimicrobial activity against Escherichia coli. Our results suggest that viviparous teleosts utilize antimicrobial peptides to reduce the risk of infection in the ovarian lumen.

Morphological basis for maternal nutrient provision to embryos in the viviparous fish Ataeniobius toweri (Teleostei: Goodeidae)

In viviparous Mexican fishes of the family Goodeidae, embryos develop in the maternal ovarian lumen. They typically absorb maternal nutrients during gestation by means of "trophotaeniae," that is, specialized, elongated extensions of the hindgut that are exposed to the fluids, which occupy the ovarian lumen. The sole exception is Ataeniobius toweri, whose embryos lack trophotaeniae but are nevertheless matrotrophic. Thus, how its embryos obtain maternal nutrients is unclear. We studied a series of non-pregnant and pregnant ovaries of A. toweri using histology to identify the mechanism of maternal-embryo nutrient transfer. By early-gestation, embryos have depleted their yolk supplies. Yolks are released into the ovarian lumen and are ingested by the developing embryos, as shown by yolk material in their digestive tracts. The embryonic gut is lined by an epithelium consisting of columnar cells with apical microvilli, providing a means for nutrient absorption. Contrary to statements in the literature, embryos develop minuscule trophotaenial rudiments that extend slightly into the ovarian lumen. These structures are formed of an absorptive epithelium that overlies a vascular stroma, similar to the trophotaeniae of other goodeids. Through late gestation, vitellogenic follicles form and oocytes are discharged into the ovarian lumen, contributing to embryonic nutrition. Thus, histological evidence suggests that embryos chiefly obtain nutrients from ingestion of yolk and maternal secretions released into the ovarian lumen. This function possibly is supplemented by uptake via the small hindgut protrusions and other absorptive surfaces (e.g., the skin and the gill epithelium). Our observations are consistent with two evolutionary interpretations of the hindgut protrusions: (a) that they are rudimentary, evolutionary precursors of trophotaeniae formed by exteriorized hindgut; and (b) that they are vestigial remnants of trophotaeniae that were lost during a switch to a form of matrotrophy involving nutrient ingestion.

Genetic differentiation in the genus Characodon: implications for conservation and taxonomy

The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.

Cubam receptor-mediated endocytosis in hindgut-derived pseudoplacenta of a viviparous teleost (Xenotoca eiseni)

Nutrient transfer from mother to embryo is essential for reproduction in viviparous animals. In the viviparous teleost Xenotoca eiseni (family Goodeidae), the intraovarian embryo intakes the maternal component secreted into the ovarian fluid via the trophotaenia. Our previous study reported that the epithelial layer cells of the trophotaenia incorporate a maternal protein via vesicle trafficking. However, the molecules responsible for the absorption were still elusive. Here, we focused on Cubam (Cubilin-Amnionless) as a receptor involved in the absorption, and cathepsin L as a functional protease in the vesicles. Our results indicated that the Cubam receptor is distributed in the apical surface of the trophotaenia epithelium and then is taken into the intracellular vesicles. The trophotaenia possesses acidic organelles in epithelial layer cells and cathepsin L-dependent proteolysis activity. This evidence does not conflict with our hypothesis that receptor-mediated endocytosis and proteolysis play roles in maternal macromolecule absorption via the trophotaenia in viviparous teleosts. Such nutrient absorption involving endocytosis is not a specific trait in viviparous fish. Similar processes have been reported in the larval stage of oviparous fish or the suckling stage of viviparous mammals. Our findings suggest that the viviparous teleost acquired trophotaenia-based viviparity from a modification of the intestinal absorption system common in vertebrates. This is a fundamental study to understand the strategic variation of the reproductive system in vertebrates.

Genetic differentiation among populations of the blackfin goodea Goodea atripinnis (Cyprinodontiformes: Goodeidae): implications for its evolutionary history

Central Mexico is characterized by a complex topography that is the result of historic and contemporary tectonic and climatic factors. These events have influenced the evolutionary history of numerous freshwater fishes in the region. Nonetheless, recent studies have shown that life-history traits and ecological characteristics of species may influence dispersal capabilities and the degree of genetic connectivity. Goodea (Cyprinodontiformes: Goodeidae) is one of the most widely distributed and environmentally tolerant genera of goodeids. In this study, the authors analysed variation in the mitochondrial cytochrome b gene to evaluate the phylogeographic relationships, genetic structure, genetic diversity and demographic history of Goodea from across its distribution range. They found low genetic differentiation and identified shared haplotypes among several regions. Geographic segregation was found in samples southwest and northeast of the Lower Lerma region, with some internal isolated groups showing phylogeographic differentiation and unique haplotypes. The AMOVA best explained genetic structure when grouped by haplogroups rather than when grouped by recognized biogeographic regions. Several regions showed null genetic diversity, raising the possibility of dispersal mediated by humans. Finally, Bayesian Skyline Plot analysis showed a population expansion for the Southwest haplogroup, except for the Armería population and sub-group II of the Northeast haplogroup. All this suggests a recent colonization of Goodea atripinnis throughout some of the biogeographic regions currently inhabited by this species.

Sharply Angled Lateral Curvature Modification in Anal Fin of a Viviparous Fish, Xenotoca variata (Cyprinodontiformes: Goodeidae)

Almost all viviparous species possess male external genitalia; for example, the mammalian penis is an intromittent organ. Some live-bearing bony fish use their anal fins to assist in mating and internal fertilization. We previously reported a male-specific asymmetric curvature at the posterior end of the anal fin in Xenotoca eiseni, a viviparous fish of the family Goodeidae. However, three other goodeid species, Xenotoca melanosoma, Zoogoneticus quitzeoensis, and Chapalichthys pardalis, examined in that study possessed lesser anal fin curvature modifications as compared to those in the anal fin of X. eiseni. Here, we report the second case of acute-angled curvature modification of the male anal fin in the family Goodeidae. We obtained a dead specimen of the goodeid species Xenotoca variata from a city zoo in Japan, and the morphological and histological analyses indicated an acute-angled asymmetric curvature of the posterior end of the anal fin in X. variata, similar to that observed in X. eiseni in the previous study. However, in our previous report, obtuse-angled modification was only observed in one other Xenotoca species, X. melanosoma, and two species belonging to other genera, Z. quitzeoensis and C. pardalis. Therefore, our findings suggest that the acute-angled curvature in the male anal fin has been developed in the genus Xenotoca.

Assessing extinction risk from geographic distribution data in Neotropical freshwater fishes

Abstract The IUCN Red List (RL) provides high-quality conservation assessments for individual species, yet the rate and scale of environmental deterioration globally challenges the conservation community to develop expedited methods for risk assessment. Here we compare threat assessments for 3,001 species of Neotropical freshwater fishes (NFF) in the IUCN–RL using readily accessible data types as proxies for extinction risk: geographic range, elevation, and species publication date. Furthermore, using geographic and taxonomic data alone, we generated preliminary conservation assessments for 2,334 NFF species currently awaiting IUCN assessment, identifying an additional 671 NFF species as potentially threatened. This number of potentially threatened species represents an increase of 59% over the number of species currently assigned to threat categories by the IUCN–RL. These results substantially expand the number of threatened NFF species from 422 currently on the IUCN RL to 1,093 species as threatened or potentially threatened, representing about 18% of all NFF species. Extinction risk is greater in species with smaller geographic ranges, which inhabit upland rivers, and which were described more recently. We propose the Central and Southern Andes, and Eastern Guiana Shield as priorities in the upcoming IUCN RL assessment of NFF species conservation risk.

Macroevolutionary dynamics of parasite diversification: A reality check

Parasitism is often invoked as a factor explaining the variation in diversification rates across the tree of life, while also representing up to half of Earth's diversity. Yet, patterns and processes of parasite diversification remain mostly unknown. In this study, we assess the patterns of parasite diversification and specifically determine the role of life-history traits (i.e. life cycle complexity and host range) and major coevolutionary events in driving diversification across eight phylogenetic datasets spanning taxonomically different parasite groups. Aware of the degree of incomplete sampling among all parasite phylogenies, we also tested the impact of sampling bias on estimates of diversification. We show that the patterns and rates of parasite diversification differ among taxa according to life cycle complexity and to some extent major host transitions. Only directly transmitted parasites were found to be influenced by an effect of major host transitions on diversification rates. Although parasitism may be a main factor responsible for heterogeneity in diversification among the tree of life, the high degree of incomplete parasite phylogenies remains an obstacle when modelling diversification dynamics. Nevertheless, we provide the first comparative test of parasite diversification, revealing some consistent patterns and insight into the processes that shape it.

Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

Mother-to-embryo vitellogenin transport in a viviparous teleost Xenotoca eiseni

Vitellogenin (Vtg), a yolk nutrient protein that is synthesized in the livers of female animals, and subsequently carried into the ovary, contributes to vitellogenesis in oviparous animals. Thus, Vtg levels are elevated during oogenesis. In contrast, Vtg proteins have been genetically lost in viviparous mammals, thus the yolk protein is not involved in their oogenesis and embryonic development. In this study, we identified Vtg protein in the livers of females during the gestation of the viviparous teleost, Xenotoca eiseni Although vitellogenesis is arrested during gestation, biochemical assays revealed that Vtg protein was present in ovarian tissues and lumen fluid. The Vtg protein was also detected in the trophotaeniae of the intraovarian embryo. Immunoelectron microscopy revealed that Vtg protein is absorbed into intracellular vesicles in the epithelial cells of the trophotaeniae. Furthermore, extraneous Vtg protein injected into the abdominal cavity of a pregnant female was subsequently detected in the trophotaeniae of the intraovarian embryo. Our data suggest that the yolk protein is one of the matrotrophic factors supplied from the mother to the intraovarian embryo during gestation in X. eiseni.

Male-specific asymmetric curvature of anal fin in a viviparous teleost, Xenotoca eiseni

Xenotoca eiseni is a viviparous teleost from the family Goodeidae. Internal fertilization occurs in this species; therefore, the male fish must transfer their sperm to the females. To this end, the males use their anal fins as external genitalia during mating. However, in goodeid species, there are a few reports of anal fin modifications functioning as genitalia. In the present study, I describe a male-specific lateral curvature with fin robe thickening on the two most posterior rays of the anal fin of X. eiseni. Morphological and behavioral analyses suggested that the lateral curvature provides a directional preference for coupling of male X. eiseni. The modification appears to be a male secondary sex characteristic. Other goodeid species Xenotoca melanosoma and Chapalichthys pardalis also possess the lateral curvature, but without robe thickening. Furthermore, Zoogoneticus quitzeoensis exhibited only curvature structure either smaller than those of other species or absent. Therefore, the anal fin curvature may not necessarily be used for internal fertilization in all species investigated in this study. However, it is still possible that it provides novel advantages during mating in certain goodeid species.