Speciation Process Research Articles

Analysis of the speciation process suggests a dual lifestyle in the plant pathogen Ralstonia solanacearum species complex

Analysis of the speciation process suggests a dual lifestyle in the plant pathogen Ralstonia solanacearum species complex

Weak reproductive isolation and extensive gene flow between Mimulus glaucescens and M. guttatus in northern California.

Barriers to reproduction are often how progress in speciation is measured. Nonetheless, an unresolved question concerns the extent to which reproductive barriers diminish gene flow between incipient species. The Sierra Nevada foothill endemic Mimulus glaucescens and the widespread M. guttatus are considered distinct species based on striking differences in vegetative morphology, but barriers to reproduction have not been previously identified, nor has gene flow between species been characterized. Here, we examined 15 potential reproductive barriers within a Northern California area of broad sympatry. Most barriers, with the exception of ecogeographic isolation, were weak or absent, and total isolation for each species was incomplete. Population genomic analyses of range-wide and broadly sympatric accessions revealed extensive gene flow between these taxa, particularly in sympatry. Despite widespread introgression, Mimulus glaucescens, emerged as monophyletic and largely comprised a single ancestry that was found at intermediate frequency within M. guttatus. This result, along with observed ecological and phenotypic differentiation, suggests that natural selection may contribute to the maintenance of distinct phenotypic forms in the earliest stages of speciation. Integrating estimates of barrier strength with direct estimates of gene flow can strengthen a more nuanced interpretation of the process of speciation in natural communities.

Genetic variability highlights the invasion route of the Lutzomyia longipalpis complex, the main vector of Visceral Leishmaniasis in Uruguay.

In the Americas, the sandfly Lutzomyia longipalpis is the main vector of the parasitic protozoa Leishmania infantum, the etiological agent of visceral leishmaniasis (VL). The Lu.longipalpis species complex is currently discontinuously distributed across the Neotropical region, from Mexico to the north of Argentina and Uruguay. During its continental spreading, it must have adapted to several biomes and temperature amplitudes, when founder events should have contributed to the high genetic divergence and geographical structure currently observed, reinforcing the speciation process. The first report of Lu.longipalpis in Uruguay was in 2010, calling the attention of Public Health authorities. Five years later, the parasite Le.infantum was recorded and in 2015 the first case of VL in canids was reported. Hitherto seven human cases by VL have been reported in Uruguay. Here, we publish the first DNA sequences from the mitochondrial genes ND4 and CYTB of Lu.longipalpis collected in Uruguay, and we used these molecular markers to investigate their genetic variability and population structure. We described four new ND4 haplotypes in a total of 98 (4/98) and one CYTB in a total of 77 (1/77). As expected, we were able to establish that the Lu.longipalpis collected in two localities (i.e. Salto and Bella Unión) from the north of Uruguay are closely related to the populations from neighbouring countries. We also propose that the possible route for the vector arrival to the region may have been through vegetation and forest corridors of the Uruguay River system, as well as it may have benefited from landscape modifications generated by commercial forestation. The ecological-scale processes shaping Lu.longipalpis populations, the identification of genetically homogeneous groups and the gene flow among them must be carefully investigated by using highly sensible molecular markers (i.e. genome wide SNPs) since it will help to the understanding of VL transmission and contribute to the planification of public policies on its control.

Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water.

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionize phylogeography.

Extinction drives a discontinuous temporal pattern of species–area relationships in a microbial microcosm system

As the most potential ecological "law", the mechanism of the species-area relationship (SAR) remains controversial. Essentially, the SAR addresses the relationship between regional area and biodiversity, shaped by speciation, extinction and dispersal processes. Extinction is the process of loss and a direct cause of species richness differences in community. Therefore, it is crucial to elucidate the role of extinction in shaping SAR. Since the extinction process has temporal dynamics, we propose the hypothesis that the occurrence of SAR should also have temporal dynamics. Here, we designed independent closed microcosm systems, in which dispersal/speciation can be excluded/neglected to reveal the role of extinction in shaping the temporal dynamics pattern of SAR. We find that extinction can shape SAR in this system independent of the dispersal and speciation process. Due to the temporal dynamics of the extinction, SAR was temporally discontinuous. The small-scale extinctions modified community structure to promote ecosystem stability and shaped SAR, while mass extinction pushed the microcosm system into the next successional stage and dismissed SAR. Our result suggested that SAR could serve as an indicator of ecosystem stability; moreover, temporal discontinuity can explain many controversies in SAR studies.

Did the Late Ordovician mass extinction event trigger the earliest evolution of ‘strophodontoid’ brachiopods?

Abstract‘Strophodontoid’ brachiopods represented the majority of strophomenide brachiopods in the Silurian and Devonian periods. They are characterized by denticles developed along the hinge line. The evolution of denticles correlated with the disappearance of dental plates and teeth and were already present when the clade originated in the Late Ordovician. Specimens ofEostropheodonta parvicostellatafrom the Kuanyinchiao Bed (early–middle Hirnantian, uppermost Ordovician) in the Hetaoba Section, Meitan, Guizhou Province, South China, display clear fossil population variation, during a process of loss of dental plates and the development of denticles. Three phenotypes ofE. parvicostellataare recognized in a single fossil bed, likely heralding a speciation process. Non‐metric multidimensional scaling (NMDS) based on five key characters of genera of the Family Leptostrophiidae shows a much wider morphospace for Silurian genera than for those in the Devonian. Phylogenetic analysis of the Family Leptostrophiidae supports the NMDS analysis and mostly tracks their geological history. The fossil population differentiation inE. parvicostellatadiscovered between the two phases of the Late Ordovician mass extinction event (LOME) linked to a major glaciation, suggests a Hirnantian origination of the ‘strophodontoid’ morphology, and links microevolutionary change to a macroevolutionary event.

Species delimitation in a recently diverged species complex of Eryngium (Apiaceae: Saniculoideae) from the Chilean Mediterranean and the Atacama Desert: morphological, environmental and molecular coalescent-based analyses

Abstract The Eryngium anomalum species complex comprises a group of annual herbs that are found in coastal areas of central-northern Chile which diverged during the Quaternary. According to current taxonomy, this complex comprises two distinct species. However, variation in their fruits suggests the presence of a hitherto undetected species. To improve our understanding of speciation processes in the complex, we follow an integrative approach using morphological, geographical, climatic and molecular data. Quantitative morphological, bioclimatic and topographic variables were analysed using uni- and multivariate statistics, and DNA sequence data from plastid and nuclear genomes using phylogenetic and coalescent-based methods. Geographical data were mapped with QGIS. The recognition of three different species in the complex is supported, one of which is new: Eryngium atacamense. These species diverged during the Quaternary in the Chilean Mediterranean and the Atacama Desert and differ in morphology, geographical distribution and climatic niche. They also show strong genetic structure as three independent lineages. Geographically and ecologically divergent habitats, mainly with different degrees of aridity, probably acted as drivers for speciation of three lineages of the E. anomalum complex during the Quaternary in the Chilean Mediterranean bioclimate.

An oligogenic architecture underlying ecological and reproductive divergence in sympatric populations

The evolutionary trajectories and genetic architectures underlying ecological divergence with gene flow are poorly understood. Sympatric timing types of the intertidal insect Clunio marinus (Diptera) from Roscoff (France) differ in lunar reproductive timing. One type reproduces at full moon, the other at new moon, controlled by a circalunar clock of yet unknown molecular nature. Lunar reproductive timing is a magic trait for a sympatric speciation process, as it is both ecologically relevant and entails assortative mating. Here, we show that the difference in reproductive timing is controlled by at least four quantitative trait loci (QTL) on three different chromosomes. They are partly associated with complex inversions, but differentiation of the inversion haplotypes cannot explain the different phenotypes. The most differentiated locus in the entire genome, with QTL support, is the period locus, implying that this gene could not only be involved in circadian timing but also in lunar timing. Our data indicate that magic traits can be based on an oligogenic architecture and can be maintained by selection on several unlinked loci.

Correction: Genetic differentiation pattern and evidence of an early speciation process in the genus Reithrodon (Rodentia: Sigmodontinae)

Correction: Genetic differentiation pattern and evidence of an early speciation process in the genus Reithrodon (Rodentia: Sigmodontinae)

Molecular and morphological analyses disclose the existence of three species of Dolichopoda (Orthoptera: Rhaphidophoridae) in the Calabria region (Italy)

ABSTRACT For a long time, Dolichopoda palpata was the only species of this genus thought to live in the cave habitats of the Calabrian region. The results of our study, based on morphological and molecular data, highlight the existence of three species in the Calabria region. In particular, our data demonstrate the occurrence of two well-separated species, one in the northern Tyrrhenian area and one in the Calabrian Ionian area, attesting to the validity of D. calabra Galvagni 1968, and the discovery of a new species, D. apollinea sp. nov. Both species appear to be geographically very limited. Dolichopoda calabra occurs in the mountain region between Scalone Pass in the north and the Savuto Valley in the south (a district called ‘Catena Costiera’), whereas D. apollinea sp. nov. appears to be distributed on the eastern slope of Pollino Massif. On the other hand, D. palpata shows a vast distribution, occurring in caves from La Sila in the north to the Aspromonte Massif in the extreme south of Calabria. About 1/3 of the Italian Dolichopoda species are present in this relatively small geographical area, supporting the importance of Calabria as a geographical region characterised by a high level of biodiversity. It shows the maximum values of genetic diversity and species richness in comparison with the rest of the Italian peninsula. This fact could be related to the palaeogeological and palaeoclimatic history of the region, as it was affected by glaciation events and eustatic movements. The combination of these two conditions that occurred during the Pliocene and Pleistocene transformed the Calabria into a vast archipelago of little islands, favouring the isolation of populations and the consequent speciation processes. http://www.zoobank.org/urn:lsid:zoobank.org:pub:AB64936E-EAEF-4730-A517-4F0C11226A94

A complex genomic architecture underlies reproductive isolation in a North American oriole hybrid zone

Natural hybrid zones provide powerful opportunities for identifying the mechanisms that facilitate and inhibit speciation. Documenting the extent of genomic admixture allows us to discern the architecture of reproductive isolation through the identification of isolating barriers. This approach is particularly powerful for characterizing the accumulation of isolating barriers in systems exhibiting varying levels of genomic divergence. Here, we use a hybrid zone between two species—the Baltimore (Icterus galbula) and Bullock’s (I. bullockii) orioles—to investigate this architecture of reproductive isolation. We combine whole genome re-sequencing with data from an additional 313 individuals amplityped at ancestry-informative markers to characterize fine-scale patterns of admixture, and to quantify links between genes and the plumage traits. On a genome-wide scale, we document several putative barriers to reproduction, including elevated peaks of divergence above a generally high genomic baseline, a large putative inversion on the Z chromosome, and complex interactions between melanogenesis-pathway candidate genes. Concordant and coincident clines for these different genomic regions further suggest the coupling of pre- and post-mating barriers. Our findings of complex and coupled interactions between pre- and post-mating barriers suggest a relatively rapid accumulation of barriers between these species, and they demonstrate the complexities of the speciation process.

Molecular and Chromosomal Evolution of DsTc1_5 and DsPogo_8 Elements (Tc1-Mariner) in Species of the Dichotomius Genus (Coleoptera: Scarabaeidae): Contributions to the Speciation Process

In Dichotomius genus, transposable elements (TE) have been related to chromosome remodeling, genomic evolution, and, possibly, to the speciation process. The objective of this study was to verify the interpopulational and interspecific conservation/variation of Tc1-Mariner elements (possibly autonomous) in Dichotomius species, aiming to identify possible contributions in the speciation process of this group. The analysis was performed on four species of Dichotomius, belonging to the Selenocopris subgenus. We verified the presence of the DsPogo_8 and DsTc1_5 elements by PCR and sequencing. We also isolated and sequenced the 28S and 16S rRNA genes aiming at the phylogenetic reconstruction of the analyzed species. Chromosomal mapping of TEs DsTc1_5 and DsPogo_8 was performed by fluorescent in situ hybridization. The results revealed the presence of the elements in the different species analyzed, except for DsTc1_5 in D. (S.) geminatus. These results suggest a vertical inheritance, with the presence of these elements in the common ancestor of these species. In the analyzed species, the nucleotide similarity of DsTc1_5 was higher than that of the 28S and 16S rRNA genes, suggesting the occurrence of horizontal transfer. The phylogenetic tree indicated that the absence of DsTc1_5 in D. (S.) geminatus is related to stochastic loss of this TE. Chromosomal mapping revealed dispersed signals, with predominance in euchromatic regions and wide variation in the chromosomal localization pattern of DsTc1_5 and DsPogo_8, both interpopulational and interspecific. This variation indicates that DsTc1_5 and DsPogo_8 may have contributed to prezygotic and postzygotic isolation, thus contributing to the speciation of these species.

Human populations are not biologically and genetically discrete.

Human populations are not biologically and genetically discrete.

Population genomics of the island thrush elucidates one of earth's great archipelagic radiations.

Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range and is arguably the world's most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted a comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea, and New Guinea to Polynesia. The island thrush's success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.

Allopatric mosaics in the Indo-West Pacific crab subfamily Chlorodiellinae reveal correlated patterns of sympatry, genetic divergence, and genitalic disparity

Molecular studies have revealed that many species once thought to be wide-ranging in the Indo-West Pacific contain allopatric mosaics of endemic lineages. These lineages provide compelling evidence that substantial time is needed to evolve isolating mechanisms sufficient to permit successful secondary sympatry, and that divergence is initiated in allopatry. In this context, questions arise regarding the nature, timing, and origin of isolating mechanisms that permit secondary sympatry. We present a phylogeny of the crab subfamily Chlorodiellinae which displays allopatric mosaics within species. These allopatric lineages typically do not have divergent male genitalia, while older sympatric lineages do. We tested the relationship between genetic distance (proxy for time), sympatry, and the divergence of male genitalic morphology. Our results suggest that male genitalic divergence is not involved in the initiation of speciation in chlorodielline crabs, having likely occurred only after isolation began in allopatry. However, morphological evolution of genitalia seemingly does play an important role in completing the process of speciation in these crabs.

Synthetic two-species allodiploid and three-species allotetraploid Saccharomyces hybrids with euploid (complete) parental subgenomes

Combination of the genomes of Saccharomyces species has great potential for the construction of new industrial strains as well as for the study of the process of speciation. However, these species are reproductively isolated by a double sterility barrier. The first barrier is mainly due to the failure of the chromosomes to pair in allodiploid meiosis. The second barrier ensures that the hybrid remains sterile even after genome duplication, an event that can restore fertility in plant interspecies hybrids. The latter is attributable to the autodiploidisation of the allotetraploid meiosis that results in sterile allodiploid spores (return to the first barrier). Occasionally, mating-competent alloaneuploid spores arise by malsegregation of MAT-carrying chromosomes. These can mate with cells of a third species resulting in aneuploid zygotes having at least one incomplete subgenome. Here we report on the construction of euploid three-species hybrids by making use of “rare mating” between a sterile S. kudriavzevii x S. uvarum allodiploid hybrid and a diploid S. cerevisiae strain. The hybrids have allotetraploid 2nScnSk nSu genomes consisting of complete sets of parental chromosomes. This is the first report on the production of euploid three-species Saccharomyces hybrids by natural mating, without genetic manipulation. The hybrids provide possibilities for studying the interactions of three allospecific genomes and their orthologous genes present in the same cell.

Dynamic properties of the pinyon pine syngameon.

This article is a Commentary on Buck et al. (2023), 237: 2435–2449.

Evolutionary history and diversity in the ball roller beetle Canthon cyanellus

To understand the evolutionary history of species, it is necessary to know the mechanisms for reproductive isolation, divergence-time between populations, and the relative action of the evolutionary forces (e.g., mutation, genetic drift, gene flow) within and between populations of the same, or closely related species. Although Canthon is one of the more diverse genera of neotropical beetles, insufficient research has been done to comprehend the divergent patterns that explain its speciation process. The absence of diagnostic morphological characters and the wide geographic variation of qualitative traits in Scarabaeinae obscures species delimitation, genealogical limits between populations, and its taxonomy. Canthon cyanellus is one of the best-known species in ecological and evolutionary aspects. It is a widely distributed species in the tropical forests of America. Also, the current deforestation has facilitated its incursion into open areas. Individuals from different populations have similar morphological characters but show wide variation in body color throughout their distribution, which makes it difficult to delimit the subspecies that comprise it. Recently, studies have been carried out to elucidate the pre-and postzygotic isolation mechanisms between populations and the historical biogeographical processes favoring cladogenesis events during the Pleistocene. Morphological variation of the male genitalia does not correspond to the phylogeographic structure. However, the morphological differences in one of the pieces of the endophallic sclerites have allowed a preliminary delimitation of some genetically differentiated clades. Finally, we consider that the joint analysis of traditional morphological taxonomy and phylogeography is important to understand the speciation process in the C. cyanellus complex.

Complete chloroplast genome sequence of Adenostemma madurense (Asteraceae)

Adenostemma madurense D.C. belongs to the family Asteraceae and is a wild annual herb found in Korea. In this study, we determined the phylogenetic position of A. madurense by identifying its complete chloroplast sequence. The result indicated a genome size of 150,054 bp, which was composed of a large single copy of 82,008 bp, two inverted repeats of 24,952 bp each, and a small singlecopy of 18,142 bp. Overall, 128 unique genes were identified, including 85 protein-coding, 35 tRNA, and 8 rRNA genes. A comparison of the A. madurense and A. lavenia chloroplast genomes revealed seven variations. Phylogenetic analysis revealed that A. madurense formed a clade with A. lavenia and had a well-supported phylogenetic relationship with Asteraceae. The first complete chloroplast genome of A. madurense was obtained, which would be helpful in explaining the process of speciation in Adenostemma and the development of molecular markers.

Homo floresiensisandHomo luzonensisare not temporally exceptional relative toHomo erectus

ABSTRACTThe presence ofHomo floresiensisandHomo luzonensisin southeast Asia 90,000 to 60,000 years ago is considered surprising by many, and has been used to support their designation as unique species and the islands they were discovered on as refugia. Here, we statistically test the null hypothesis thatH. floresiensisandH.luzonensisrepresent temporally uninterrupted occurrences relative toHomo erectus. We do this using the ‘surprise test’ for the exceptionality of a new record. Results demonstrate thatH. floresiensisandH. luzonensisare not temporally distinct relative toH. erectus. Their late persistence should, therefore, not be considered surprising, they cannot reliably be inferred to be outside ofH. erectus’ temporal range, and – temporally – the islands of Luzon and Flores are not supported as refugia. Similarly, lateH. erectusat Ngandong, Java, is not demonstrated to be temporally distinct relative to earlier, principally mainland‐Asian,H. erectus. Further, we demonstrate that substantial numbers of fossil discoveries would be needed beforeH. floresiensisandH. luzonensisare outside ofH. erectus’expected temporal range. IfH. floresiensisandH. luzonensisare descended fromH. erectuspopulations, our results point toward either geographic processes of allopatric speciation or behavioural processes leading to a sympatric speciation event.