Genetic Distance Research Articles

Detection and characterization of H5N1 HPAIV in environmental samples from a dairy farm.

The recent expansion of HPAIV H5N1 infections in terrestrial mammals in the Americas, most recently including the outbreak in dairy cattle, emphasizes the critical need for better epidemiological monitoring of zoonotic diseases. In this work, we detected, isolated, and characterized the HPAIV H5N1 from environmental swab samples collected from a dairy farm in the state of Kansas, USA. Genomic sequencing of these samples uncovered two distinctive substitutions in the PB2 (E249G) and NS1 (R21Q) genes which are rare and absent in recent 2024 isolates of H5N1 circulating in the mammalian and avian species. Additionally, approximately 1.7% of the sequence reads indicated a PB2 (E627K) substitution, commonly associated with virus adaptation to mammalian hosts. Phylogenetic analyses of the PB2 and NS genes demonstrated more genetic identity between this environmental isolate and the 2024 human isolate (A/Texas/37/2024) of H5N1. Conversely, HA and NA gene analyses revealed a closer relationship between our isolate and those found in other dairy cattle with almost 100% identity, sharing a common phylogenetic subtree. These findings underscore the rapid evolutionary progression of HPAIV H5N1 among dairy cattle and reinforces the need for more epidemiological monitoring which can be done using environmental sampling.

Induced genetic diversity through mutagenesis in wheat gene pool and significant use of SCoT markers to underpin key agronomic traits

BackgroundThis research explores the efficacy of mutagenesis, specifically using sodium azide (SA) and hydrazine hydrate (HZ) treatments, to introduce genetic diversity and enhance traits in three wheat (Triticum aestivum L.) genotypes. The experiment entails subjecting the seeds to different doses of SA and HZ and cultivating them in the field for two consecutive generations: M1 (first generation) and M2 (second generation). We then employed selective breeding techniques with Start Codon Targeted (SCoT) markers to select traits within the wheat gene pool. Also, the correlation between SCoT markers and specific agronomic traits provides insights into the genetic mechanisms underlying mutagenesis-induced changes in wheat.ResultsIn the study, eleven genotypes were derived from parent varieties Sids1, Sids12, and Giza 168, and eight mutant genotypes were selected from the M1 generation and further cultivated to establish the M2 generation. The results revealed that various morphological and agronomical characteristics, such as plant height, spikes per plant, spike length, spikelet per spike, grains per spikelet, and 100-grain weight, showed increases in different genotypes from M1 to M2. SCoT markers were employed to assess genetic diversity among the eleven genotypes. The bioinformatics analysis identified a correlation between SCoT markers and the transcription factors ABSCISIC ACID INSENSITIVE3 (ABI3) and VIVIPAROUS1 (VP1), crucial for plant development, growth, and stress adaptation. A comprehensive examination of genetic distance and the function identification of gene-associated SCoT markers may provide valuable insights into the mechanisms by which SA and HZ act as mutagens, enhancing wheat agronomic qualities.ConclusionsThis study demonstrates the effective use of SA and HZ treatments to induce gene diversity through mutagenesis in the wheat gene pool, resulting in the enhancement of agronomic traits, as revealed by SCoT markers. The significant improvements in morphological and agronomical characteristics highlight the potential of mutagenesis techniques for crop improvement. These findings offer valuable information for breeders to develop effective breeding programs to enhance wheat quality and resilience through increased genetic diversity.

Genetic variability of Roma population in Serbia: The perspective from autosomal STR markers.

Genetic variability of Roma population was shaped by the strong influence of genetic drift and gene flow during the migrations from their ancestral homeland in Indian subcontinent towards Europe. In addition, social stigmatization in many European countries, as a consequence of different cultural heritage and social practices, induced further genetic differentiation and sub structuring within the population. Although many populations genetic studies on European Roma were carried out, the genetic structure of the Serbian Roma has not been described yet, since only the modest number of individuals from this territory was analyzed. The main aim of this study was the characterization of genetic variability of the Roma and the assessment of intrapopulation genetic differentiation based on the analysis of 21 autosomal STR loci of 259 self-identified unrelated individuals from Serbia. Intrapopulation analysis revealed divergence of Roma groups illustrating the effect of the historical events after their arrival on Balkan Peninsula and emphasizing significance of the religious affiliation on admixture with autochthonous population. Genetic distance analysis showed the greatest similarity of the studied population with the Middle Eastern populations, while South Asian and European population were more distant. Our results demonstrate that Roma groups in this region of Balkan Peninsula do not represent completely isolated, but rather admixed populations with different proportion of gene flow with other Roma and non-Roma groups.

First Insight into the Phylogenetic Diversity of Bovicola caprae Infesting Goats of Different Agro-climatic Locations in India.

Bovicola caprae is an important obligate ectoparasite of goats worldwide including India. The present study aimed at the molecular confirmation, phylogenetics and population structure analyses of B. caprae infesting goats of three different agro-climatic locations in India, by targeting the mitochondrial cytochrome C oxidase subunit 1 (cox1) genetic marker. The phylogenetic tree exhibited the presence of two different lineages of B. caprae. The sequences generated herein clustered in lineage 2 along with theGenBank™ archived sequences from China and Iran. The sequences generated herein also showed the circulation of sub-lineages of B. caprae in India based on the analysis of pairwise genetic distances between sequences and median-joining haplotype network. The population structure analyses revealed low nucleotide (0.00353 ± 0.00291 and 0.02694 ± 0.00363) and high haplotype (0.667 ± 0.314 and 0.618 ± 0.104) diversities for the present study isolates as well as for the complete dataset, respectively, which evinced a recent demographic expansion. High genetic differentiation (FST value = 0.97826) and low gene flow (Nm = 0.00556) were also recorded in the different lineages/populations. In conclusion, the present study addressed the research gap and provided the first insight into the phylogenetics of the goat louse B. caprae and highlighted the circulation of sub-lineages of the ectoparasite in India.

Isolation and characterization of a novel Bacillus cereus bacteriophage vBce-DP7

Foodborne pathogens have become a major concern for public health. Bacillus cereus, a representative foodborne pathogen, is particularly challenging due to its ability to cause food poisoning and its resilient spores that are difficult to completely eradicate. Therefore, it is crucial to develop measures to prevent and control B. cereus. Bacteriophages, which are high specific towards their host strains and cannot infect eukaryotes, have proven to be effective in combating foodborne pathogens and are safe for human use. In this study, we isolated and characterized a novel bacteriophage named vBce-DP7 that specifically targets B. cereus strains belonging to three different sequence types (STs). Phage vBce-DP7 is a lytic one and has a short latent time of only 15 minutes. Moreover, it exhibited a good temperature tolerance, retaining high activity across a broad range of 4 - 55 °C. Additionally, its activity remains unaffected within a wide pH range spanning from 2 - 10. Interestingly, with only 4% genetic similarity with known bacteriophages, vBce-BP7 shows a possible classification on a family level though it shares many similar functional proteins with Salasmaviridae bacteriophages. Taken together, vBce-BP7 demonstrates its significant potential for further exploration in terms of phage diversity and its application in controlling B. cereus.

Comparing Gold-Standard Sanger Sequencing with Two Next-Generation Sequencing Platforms of HIV-1 gp160 Single Genome Amplicons.

Our goal was to assess the accuracy of next generation sequencing (NGS) compared with Sanger. We performed single genome amplification (SGA) of HIV-1 gp160 on extracted tissue DNA from two HIV+ individuals. Amplicons (n = 30) were sequenced with Sanger or reamplified with barcoded primers and pooled before sequencing using Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PB). For each amplicon, a consensus sequence for NGS reads was obtained by (1) mapping reads to the Sanger sequence when available ("reference-based") or (2) mapping reads to a "pseudo-reference" sequence, i.e., a consensus sequence of a subset of NGS reads ("reference-free"). PB reads were clustered based on genetic similarity. A Sanger consensus sequence was obtained for 23/30 amplicons, for which all NGS consensus sequences were identical (n = 9) or nearly identical (n = 14) compared with Sanger. For the nine mismatches between Sanger/NGS, the nucleotide in the NGS sequence matched all other sequences from that patient. Of the 7/30 amplicons without a Sanger sequence, NGS sequences had ≥35 ambiguous calls in five amplicons and 0 ambiguitiesin two amplicons. Analysis of the electropherograms showed failure of a single sequencing primer for the latter two amplicons (consistent with a single template) and overlapping peaks for the other five (consistent with multiple templates). Clustering results closely followed the Sanger/NGS consensus results, where amplicons derived from a single template also had a single cluster and vice versa (with one exception, which could be the result of barcode misidentification). Representative sequences from the clusters contained 2-13 differences compared with Sanger/NGS. In summary, we show that both ONT and PB can produce amplicon consensus sequences with similar or higher accuracy compared with Sanger and, importantly, without the need for a known reference sequence. Clustering could be useful in some circumstances to predict or confirm the presence of multiple starting templates.

AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters

Molecular surveillance of viral pathogens and inference of transmission networks from genomic data play an increasingly important role in public health efforts, especially for HIV-1. For many methods, the genetic distance threshold used to connect sequences in the transmission network is a key parameter informing the properties of inferred networks. Using a distance threshold that is too high can result in a network with many spurious links, making it difficult to interpret. Conversely, a distance threshold that is too low can result in a network with too few links, which may not capture key insights into clusters of public health concern. Published research using the HIV-TRACE software package frequently uses the default threshold of 0.015 substitutions/site for HIV pol gene sequences, but in many cases, investigators heuristically select other threshold parameters to better capture the underlying dynamics of the epidemic they are studying. Here, we present a general heuristic scoring approach for tuning a distance threshold adaptively, which seeks to prevent the formation of giant clusters. We prioritize the ratio of the sizes of the largest and the second largest cluster, maximizing the number of clusters present in the network. We apply our scoring heuristic to outbreaks with different characteristics, such as regional or temporal variability, and demonstrate the utility of using the scoring mechanism’s suggested distance threshold to identify clusters exhibiting risk factors that would have otherwise been more difficult to identify. For example, while we found that a 0.015 substitutions/site distance threshold is typical for US-like epidemics, recent outbreaks like the CRF07_BC subtype among men who have sex with men (MSM) in China have been found to have a lower optimal threshold of 0.005 to better capture the transition from injected drug use (IDU) to MSM as the primary risk factor. Alternatively, in communities surrounding Lake Victoria in Uganda, where there has been sustained heterosexual transmission for many years, we found that a larger distance threshold is necessary to capture a more risk factor-diverse population with sparse sampling over a longer period of time. Such identification may allow for more informed intervention action by respective public health officials.

Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies.

Range contraction and expansion from glaciation has led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units.

EquCab_Finn: A new reference genome assembly for the domestic horse, Finnhorse.

Finnhorse is Finland's native and national horse breed and it has genetic affinities to northern European and Asian horses. It has historical importance for agriculture, forest work and transport and as a war horse. Finnhorse has four breeding sections in the studbook and is under conservation and characterisation efforts. We sequenced and annotated the genome of a Finnhorse mare from the working horse section using PacBio and Omni-C data. This genome can complement the existing Thoroughbred reference genome (EquCab 3.0) and facilitate genetic studies of horses from northern Eurasia. We assembled 2.4 Gb of the genome with an N50 scaffold length of 83.8 Mb and the genome annotation resulted in a total of 19 748 protein coding genes of which 1200 were Finnhorse specific. The assembly has high quality and synteny with the current horse reference genome. We manually curated five genes of interest and deposited the final assembly in the European Nucleotide Archive under the accession no. PRJEB71364.

Dendrodorididae (Heterobranchia, Nudibranchia) from Persian Gulf with a description of a new species of Doriopsilla and remarks on the family

The family Dendrodorididae has a global distribution, with prevalence in tropical and subtropical intertidal zones. Three species of Dendrodorididae were collected from the intertidal zone of the northern coast of the Persian Gulf in Iran. Based on anatomical, histological, and molecular investigations they can be assigned to Dendrodoris fumata, Dendrodoris nigra, and a new species of Doriopsilla, D. aroni sp. nov. Molecular analyses of CO1 and 16S, including all genera of Dendrodorididae, members of the sister taxon Phyllidiidae, and other dorid outgroups resulted in a polyphyletic genus Dendrodoris, which is in contrast to the nuclear gene studies. Our molecular results confirm the differentiation between Dendrodoris rubra and D. fumata. Dendrodoris nigra, D. fumata, and D. krusensternii each consist of several clades, indicating cryptic species complexes requiring further investigation. We describe the presence of bacteria for the first time in the vestibular gland of D. fumata. Validation of the specimens of Doriopsilla from the Persian Gulf as a new species is supported by haplotype networking, genetic distance, and ABGD analyses of mitochondrial genes. Our CO1 analysis confirms a previous hypothesis that Cariopsilla is a junior synonym of Doriopsilla.

Dendrodorididae (Heterobranchia, Nudibranchia) from Persian Gulf with a description of a new species of Doriopsilla and remarks on the family

The family Dendrodorididae has a global distribution, with prevalence in tropical and subtropical intertidal zones. Three species of Dendrodorididae were collected from the intertidal zone of the northern coast of the Persian Gulf in Iran. Based on anatomical, histological, and molecular investigations they can be assigned to Dendrodoris fumata, Dendrodoris nigra, and a new species of Doriopsilla, D. aroni sp. nov. Molecular analyses of CO1 and 16S, including all genera of Dendrodorididae, members of the sister taxon Phyllidiidae, and other dorid outgroups resulted in a polyphyletic genus Dendrodoris, which is in contrast to the nuclear gene studies. Our molecular results confirm the differentiation between Dendrodoris rubra and D. fumata. Dendrodoris nigra, D. fumata, and D. krusensternii each consist of several clades, indicating cryptic species complexes requiring further investigation. We describe the presence of bacteria for the first time in the vestibular gland of D. fumata. Validation of the specimens of Doriopsilla from the Persian Gulf as a new species is supported by haplotype networking, genetic distance, and ABGD analyses of mitochondrial genes. Our CO1 analysis confirms a previous hypothesis that Cariopsilla is a junior synonym of Doriopsilla.

Microdous hanlini (Gobiiformes: Odontobutidae), a new species of the fine-toothed sleepers from Guangxi, China

Microdous (Gobiiformes: Odontobutidae) is a genus of freshwater sleepers distributed in southern China and Vietnam. There are two described species in this genus, M. chalmersi widely distributed in Hainan Island and Guangxi province of China and M. amblyrhynchos with a very restricted distribution range in Baise, Guangxi. It has been reported that M. chalmersi of Guangxi might be a cryptic species, which is different from M. chalmersi of Hainan. Here, we describe the cryptic species from Guangxi as a new species, Microdous hanlini, and compare it with the other species of Microdous. Microdous hanlini can be distinguished from M. chalmersi by its wider head (head width/head length = 0.51–0.58 vs. 0.48–0.53 in M. chalmersi) and wider interorbital width (interorbital width/head length = 0.15–0.19 vs. 0.09–0.13 in M. chalmersi). Microdous hanlini can be distinguished from M. amblyrhynchos by its longer snout, (snout length/head length = 0.29–0.35 vs. 0.26–0.28 in M. amblyrhynchos); slenderer head (head width/head length = 0.51–0.58 vs. 0.61–0.65); and protruding eyes (vs. not protruding). Phylogenetics analyses based on partial sequence of cytochrome c oxidase subunit I (COI) gene (~1500 bp) showed that M. hanlini, M. chalmersi and M. amblyrhynchos formed reciprocal monophyletic clades and M. hanlini is more closely related to M. amblyrhynchos than to M. chalmersi. Genetic distance between the three species is greater than the interspecific distance between some species of Odontobutis.

The Characteristic of HBV Quasispecies Is Related to Occult HBV Infection of Infants Born to Highly Viremic Mothers

Although a combination of immunoprophylaxis and antiviral therapy can effectively prevent mother-to-child transmission (MTCT) of hepatitis B virus (HBV), a considerable number of infants born to highly viremic mothers still develop occult HBV infection (OBI). To uncover the virological factor and risk predictor for OBI in infants, we found that the diversity and complexity of maternal HBV quasispecies in the case group were lower than those in the control group. Mutations with significant differences between the two groups were most enriched in the NTCPbd and PreC regions. Genetic distance at the amino-acid level of the PreC region, especially the combination of three amino-acid mutations in the PreC region, could strongly predict the risk of OBI in infants. HBV quasispecies in OBI infants were highly complex, and the non-synonymous substitutions were mainly found in the RT and HBsAg regions. The sK47E (rtQ55R) and sP49L mutations in OBI infants might contribute to OBI through inhibiting the production of HBV DNA and HBsAg, respectively. This study found the potential virological factors and risk predictors for OBI in infants born to highly viremic mothers, which might be helpful for controlling OBI in infants.

The Characteristic of HBV Quasispecies Is Related to Occult HBV Infection of Infants Born to Highly Viremic Mothers

Although a combination of immunoprophylaxis and antiviral therapy can effectively prevent mother-to-child transmission (MTCT) of hepatitis B virus (HBV), a considerable number of infants born to highly viremic mothers still develop occult HBV infection (OBI). To uncover the virological factor and risk predictor for OBI in infants, we found that the diversity and complexity of maternal HBV quasispecies in the case group were lower than those in the control group. Mutations with significant differences between the two groups were most enriched in the NTCPbd and PreC regions. Genetic distance at the amino-acid level of the PreC region, especially the combination of three amino-acid mutations in the PreC region, could strongly predict the risk of OBI in infants. HBV quasispecies in OBI infants were highly complex, and the non-synonymous substitutions were mainly found in the RT and HBsAg regions. The sK47E (rtQ55R) and sP49L mutations in OBI infants might contribute to OBI through inhibiting the production of HBV DNA and HBsAg, respectively. This study found the potential virological factors and risk predictors for OBI in infants born to highly viremic mothers, which might be helpful for controlling OBI in infants.

Atypical structure of the nuclear membrane, distribution of nuclear pores and lamin B1 in spermatozoa of patients with complete and partial globozoospermia

Globozoospermia is a form of male infertility characterized by spermatozoa with spherical heads lacking acrosomes. The aim of this study was to evaluate ultrastructural and molecular defects in different types of globozoospermia. Semen samples from 12 infertile patients (9 with complete globozoospermia and 3 with partial globozoospermia) and 10 normozoospermic men (control) were examined by transmission electron microscopy and immunocytochemistry with antibodies against lamin B1. The presence of lamin A and progerin was assessed by reverse transcription-PCR. Whole exome sequencing was performed in three patients. In semen samples with complete and partial globozoospermia, lamin B1 was observed at the periphery of sperm nuclei, whereas lamin A and progerin were absent. Nuclear envelope pores were found in spermatozoa from both patient groups, regardless of morphology and chromatin condensation, in contrast to the control group. Non-condensed chromatin was present in 51%–81% of cases of complete globozoospermia and in 36%–79% of cases of partial globozoospermia. Homozygous DPY19L2 and SPATA16 variants were identified in two patients with partial globozoospermia and one patient with complete globozoospermia. An atypical nuclear membrane with abnormal nuclear pore distribution and lamin B1 localization was observed in spermatozoa from patients with both complete and partial globozoospermia. The genetic defects in the DPY19L2 and SPATA16 genes detected in patients from both globozoospermic groups suggest a generalized disruption of nuclear structure in globozoospermia, highlighting the genetic and phenotypic similarities between complete and partial globozoospermia.

Taxonomic resolution of the hillstream suck-loach Beaufortia pingi species group (Cypriniformes, Gastromyzontidae) and two new species from Southwest China– Beaufortia granulopinna and Beaufortia viridis

Two new species, Beaufortia granulopinna and Beaufortia viridis, are described from the upper Pearl River system in southwest China. Both species share the characteristics of the Beaufortia pingi species group, including prominent vertical stripes on the lateral body and pinnate-type lower lips, distinguishing them from other Beaufortia species. Beaufortia granulopinna is differentiated from other species in the group by possessing a unique set of characteristics: the presence of well-developed prominent tubercles on the first 6–9 pectoral fin rays in adults; and a significant proportion (54.76%) of individuals experiencing blurriness or absence of vertical stripes in the mid-section of the lateral body upon reaching adulthood. The minimum interspecific genetic distance within the genus based on mitochondrial cytb gene sequences is 10.80%. Beaufortia viridis is distinguished from other species in the group by consistently exhibiting vertical stripes of uniform length, width, and spacing across all stages of growth; the absence of tubercles on the branched rays of pectoral fins; and a body coloration of dark cyan to green. The minimum interspecific genetic distance within the genus based on mitochondrial cytb gene sequences is 4.60%. Molecular phylogenetic results confirm that the Beaufortia pingi species group forms a monophyletic clade, which is congruent with morphological classification findings. This study also addresses and resolves the taxonomic ambiguity surrounding Beaufortia pingi and Beaufortia zebroida, providing a redescription of these taxa.

Taxonomic resolution of the hillstream suck-loach Beaufortia pingi species group (Cypriniformes, Gastromyzontidae) and two new species from Southwest China– Beaufortia granulopinna and Beaufortia viridis

Two new species, Beaufortia granulopinna and Beaufortia viridis, are described from the upper Pearl River system in southwest China. Both species share the characteristics of the Beaufortia pingi species group, including prominent vertical stripes on the lateral body and pinnate-type lower lips, distinguishing them from other Beaufortia species. Beaufortia granulopinna is differentiated from other species in the group by possessing a unique set of characteristics: the presence of well-developed prominent tubercles on the first 6–9 pectoral fin rays in adults; and a significant proportion (54.76%) of individuals experiencing blurriness or absence of vertical stripes in the mid-section of the lateral body upon reaching adulthood. The minimum interspecific genetic distance within the genus based on mitochondrial cytb gene sequences is 10.80%. Beaufortia viridis is distinguished from other species in the group by consistently exhibiting vertical stripes of uniform length, width, and spacing across all stages of growth; the absence of tubercles on the branched rays of pectoral fins; and a body coloration of dark cyan to green. The minimum interspecific genetic distance within the genus based on mitochondrial cytb gene sequences is 4.60%. Molecular phylogenetic results confirm that the Beaufortia pingi species group forms a monophyletic clade, which is congruent with morphological classification findings. This study also addresses and resolves the taxonomic ambiguity surrounding Beaufortia pingi and Beaufortia zebroida, providing a redescription of these taxa.

Phylogeny and genetic diversity of Echinometra sea urchin in Taiwan

ABSTRACT Four closely related Echinometra species exist in the Indo-Pacific region, but little is known about their population genetics in Taiwan, an area rich in marine biodiversity. Echinometra dominates the Douziping coral reef off Liuqiu Island, where urchin barrens are also present. To understand the relationship between Echinometra species and urchin barrens, we investigated the genetic diversity of Echinometra species in Taiwan by using a nondestructive DNA extraction method on the spines of sea urchins. Mitochondrial DNA results showed that E. sp. C is the dominant species in Taiwan, with relatively high interspecific genetic distance. The E. sp. C is the only species in Douziping, and its population is expanding in accordance with the significantly low R2 value, the significantly negative Fu’s Fs values, and mismatch distribution analysis results. Gene flow estimates between the urchin populations in Taiwan and those in the neighbouring waters of Okinawa suggested that the Kuroshio Current could play an important role in Echinometra dispersal. This implies strongly connectivity between these populations. This study reports the first case of E. sp. C-associated urchin barrens in the tropics.

An assemblage-level comparison of genetic diversity and population genetic structure between island and mainland ant populations.

Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, for example, typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California. As expected, island populations (from Santa Cruz Island) had lower expected heterozygosity and Watterson's theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision. Within the focal assemblage, pairwise Fst values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal population differences across an assemblage of interacting species, and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine conspecific population pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes.

Phylogeny and genetic diversity of Echinometra sea urchin in Taiwan

ABSTRACT Four closely related Echinometra species exist in the Indo-Pacific region, but little is known about their population genetics in Taiwan, an area rich in marine biodiversity. Echinometra dominates the Douziping coral reef off Liuqiu Island, where urchin barrens are also present. To understand the relationship between Echinometra species and urchin barrens, we investigated the genetic diversity of Echinometra species in Taiwan by using a nondestructive DNA extraction method on the spines of sea urchins. Mitochondrial DNA results showed that E. sp. C is the dominant species in Taiwan, with relatively high interspecific genetic distance. The E. sp. C is the only species in Douziping, and its population is expanding in accordance with the significantly low R2 value, the significantly negative Fu’s Fs values, and mismatch distribution analysis results. Gene flow estimates between the urchin populations in Taiwan and those in the neighbouring waters of Okinawa suggested that the Kuroshio Current could play an important role in Echinometra dispersal. This implies strongly connectivity between these populations. This study reports the first case of E. sp. C-associated urchin barrens in the tropics.