Species diversity

@article{connell1964the,
    author = "Connell, Joseph H. and Orias, Eduardo",
    title = "The Ecological Regulation of Species Diversity",
    year = "1964",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/282335",
    doi = "10.1086/282335",
    number = "903",
    pages = "399-414",
    volume = "98"
}

@misc{connell1964the1,
    author = "Connell, J. H. and Orias, E",
    title = "The ecological regulation of species diversity",
    year = "1964",
    howpublished = "American Naturalist, v. 98, p. 399-414",
    note = "talkorigins\_source = {true}; raw\_reference = {Connell, J. H., and Orias, E., 1964, The ecological regulation of species diversity: American Naturalist, v. 98, p. 399-414.}"
}

@misc{erhlich1969differentiations2,
    author = "Erhlich, P. R. and Raven, P. H",
    title = "Differentiations in populations",
    year = "1969",
    howpublished = "Science, v. 165, p. 1228-1231",
    note = "talkorigins\_source = {true}; raw\_reference = {Erhlich, P. R., and Raven, P. H., 1969, Differentiations in populations: Science, v. 165, p. 1228-1231.}"
}

Ecological drift causes species abundances to fluctuate randomly, lowering diversity within communities and increasing differences among otherwise equivalent communities. Despite broad interest in ecological drift, ecologists have little experimental evidence of its consequences in nature, where competitive forces modulate species abundances. We manipulated drift by imposing 40-fold variation in the size of experimentally assembled annual plant communities and holding their edge-to-interior ratios comparable. Drift over three generations was greater than predicted by neutral models, causing high extinction rates and fast divergence in composition among smaller communities. Competitive asymmetries drove populations of most species to small enough sizes that demographic stochasticity could markedly influence dynamics, increasing the importance of drift in communities. The strong effects of drift occurred despite stabilizing niche differences, which cause species to have greater population growth rates when at low local abundance. Overall, the importance of ecological drift appears greater in non-neutral communities than previously recognized, and varies with community size and the type and strength of density dependence.

@article{doi101098rspb20170507,
    author = "Gilbert, B. and Levine, J.",
    title = "Ecological drift and the distribution of species diversity",
    year = "2017",
    journal = "Proceedings of the Royal Society B: Biological Sciences",
    abstract = "Ecological drift causes species abundances to fluctuate randomly, lowering diversity within communities and increasing differences among otherwise equivalent communities. Despite broad interest in ecological drift, ecologists have little experimental evidence of its consequences in nature, where competitive forces modulate species abundances. We manipulated drift by imposing 40-fold variation in the size of experimentally assembled annual plant communities and holding their edge-to-interior ratios comparable. Drift over three generations was greater than predicted by neutral models, causing high extinction rates and fast divergence in composition among smaller communities. Competitive asymmetries drove populations of most species to small enough sizes that demographic stochasticity could markedly influence dynamics, increasing the importance of drift in communities. The strong effects of drift occurred despite stabilizing niche differences, which cause species to have greater population growth rates when at low local abundance. Overall, the importance of ecological drift appears greater in non-neutral communities than previously recognized, and varies with community size and the type and strength of density dependence.",
    url = "https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2017.0507",
    doi = "10.1098/rspb.2017.0507",
    is_oa = "true",
    number = "1855",
    pages = "20170507",
    semanticscholar_citation_count = "173",
    semanticscholar_id = "357621918a10eefdfa8f55f60cf1f2590cf8a7c2",
    volume = "284"
}

The worldwide loss of species diversity brings urgency to understanding how diverse ecosystems maintain stability. Whereas early ecological ideas and classic observations suggested that stability increases with diversity, ecological theory makes the opposite prediction, leading to the long-standing "diversity-stability debate." Here, we show that this puzzle can be resolved if growth scales as a sublinear power law with biomass (exponent <1), exhibiting a form of population self-regulation analogous to models of individual ontogeny. We show that competitive interactions among populations with sublinear growth do not lead to exclusion, as occurs with logistic growth, but instead promote stability at higher diversity. Our model realigns theory with classic observations and predicts large-scale macroecological patterns. However, it makes an unsettling prediction: Biodiversity loss may accelerate the destabilization of ecosystems.

@article{doi101126scienceadg8488,
    author = "Hatton, Ian and Mazzarisi, Onofrio and Altieri, Ada and Smerlak, Matteo",
    title = "Diversity begets stability: Sublinear growth and competitive coexistence across ecosystems",
    year = "2024",
    journal = "Science",
    abstract = {The worldwide loss of species diversity brings urgency to understanding how diverse ecosystems maintain stability. Whereas early ecological ideas and classic observations suggested that stability increases with diversity, ecological theory makes the opposite prediction, leading to the long-standing "diversity-stability debate." Here, we show that this puzzle can be resolved if growth scales as a sublinear power law with biomass (exponent <1), exhibiting a form of population self-regulation analogous to models of individual ontogeny. We show that competitive interactions among populations with sublinear growth do not lead to exclusion, as occurs with logistic growth, but instead promote stability at higher diversity. Our model realigns theory with classic observations and predicts large-scale macroecological patterns. However, it makes an unsettling prediction: Biodiversity loss may accelerate the destabilization of ecosystems.},
    url = "https://doi.org/10.1126/science.adg8488",
    doi = "10.1126/science.adg8488",
    openalex = "W4392796813",
    references = "doi101111ecog05778, doi101126scienceaac6284"
}

Abstract. Banaybanay DP, Amparado OA, Morilla LJG, Estaño LA. 2024. Species diversity of Odonata in the urban ecosystem of Iligan City, Philippines. Biodiversitas 25: 890-899. Urbanization impacts ecosystem function and services, resulting in changes in ecological processes, increasing human population, and biodiversity loss. This threat may influence Odonata species' abundance, diversity, and distribution in freshwater habitats. The survey of Odonata in the urban ecosystem in Iligan City was carried out from December 2022 to March 2023 to determine the species diversity, abundance, endemism, distribution, and their correlation to various environmental parameters in freshwater habitat in this area. Field sampling was conducted in six identified barangays: Barangay Tubod, Bagong Silang, Del Carmen, Villa Verde, Poblacion, and Ubaldo Laya. The study recorded 569 individuals consisting of two major Odonate families, the Family Libellulidae, comprising nine species: Acisoma panorpoides, Brachydiplax chalybea, Crocothemis servilia, Diplacodes trivialis, Neurothemis terminata, Neurothemis ramburii, Orthetrum sabina, Rhodothemis rufa and Trithemis aurora; and Family Coenagrionidae with four species: Agriocnemis femina, Ceriagrion lieftincki, Ischnura senegalensis and Pseudagrion pilidorsum. Among the recorded species, I. senegalensis (34.80%) was found to be the most abundant species, followed by A. femina (32.51%) and O. sabina (10.54%), which are encountered in all sampling sites. Meanwhile, the low diversity and low endemism (7.69%) were recorded in all sampling areas, with C. lieftincki as the only Philippine endemic recorded in Iligan City Wet Park and Barangay Bagong Silang. Canonical correspondence analysis reveals that environmental factors such as air temperature, water temperature, water pH, water turbidity, and relative humidity are crucial parameters in determining the assemblage of Odonata. Overall, urban ecosystems in Iligan City are dominated by oriental species, signifying that the areas are heavily disturbed. Therefore, urgent management of urban ecosystems is required to enhance the city's ecological health, sustainability, and insect biodiversity.

@article{doi1013057biodivd250249,
    author = "Banaybanay, Dranreb P. and Amparado, Olive A. and Morilla, L. J. G. and Estaño, L.",
    title = "Species diversity of Odonata in the urban ecosystem of Iligan City, Philippines",
    year = "2024",
    journal = "Biodiversitas Journal of Biological Diversity",
    abstract = "Abstract. Banaybanay DP, Amparado OA, Morilla LJG, Estaño LA. 2024. Species diversity of Odonata in the urban ecosystem of Iligan City, Philippines. Biodiversitas 25: 890-899. Urbanization impacts ecosystem function and services, resulting in changes in ecological processes, increasing human population, and biodiversity loss. This threat may influence Odonata species' abundance, diversity, and distribution in freshwater habitats. The survey of Odonata in the urban ecosystem in Iligan City was carried out from December 2022 to March 2023 to determine the species diversity, abundance, endemism, distribution, and their correlation to various environmental parameters in freshwater habitat in this area. Field sampling was conducted in six identified barangays: Barangay Tubod, Bagong Silang, Del Carmen, Villa Verde, Poblacion, and Ubaldo Laya. The study recorded 569 individuals consisting of two major Odonate families, the Family Libellulidae, comprising nine species: Acisoma panorpoides, Brachydiplax chalybea, Crocothemis servilia, Diplacodes trivialis, Neurothemis terminata, Neurothemis ramburii, Orthetrum sabina, Rhodothemis rufa and Trithemis aurora; and Family Coenagrionidae with four species: Agriocnemis femina, Ceriagrion lieftincki, Ischnura senegalensis and Pseudagrion pilidorsum. Among the recorded species, I. senegalensis (34.80\%) was found to be the most abundant species, followed by A. femina (32.51\%) and O. sabina (10.54\%), which are encountered in all sampling sites. Meanwhile, the low diversity and low endemism (7.69\%) were recorded in all sampling areas, with C. lieftincki as the only Philippine endemic recorded in Iligan City Wet Park and Barangay Bagong Silang. Canonical correspondence analysis reveals that environmental factors such as air temperature, water temperature, water pH, water turbidity, and relative humidity are crucial parameters in determining the assemblage of Odonata. Overall, urban ecosystems in Iligan City are dominated by oriental species, signifying that the areas are heavily disturbed. Therefore, urgent management of urban ecosystems is required to enhance the city's ecological health, sustainability, and insect biodiversity.",
    url = "https://smujo.id/biodiv/article/download/17119/7557",
    doi = "10.13057/biodiv/d250249",
    is_oa = "true",
    number = "2",
    semanticscholar_id = "6f1d7c8b91e3b7fb4c1eb913d1c9a540e85b7cc0",
    volume = "25"
}

Coastal dune plants play an important role in maintaining the stability of coastal dune areas. Artemisia stelleriana Besser. is a coastal dune plant with a northern distribution, and populations are scattered and isolated in Japan due to habitat loss, leading to its classification as an endangered species in several prefectures. However, very few ecological and genetic studies of A. stelleriana have been conducted worldwide. This study was performed to investigate the self‐compatibility, flower structure, and flowering phenology, seed thalassochory potential, and clonal propagation ability of A. stelleriana, along with the genetic diversity of four populations in Niigata Prefecture. Our results showed that A. stelleriana is self‐compatible, with a flower head composed of female and hermaphrodite florets that have overlapping flowering periods. The species also exhibits a relatively short seed floating period, which leads to limited seed dispersal by sea currents, and possesses a weak clonal structure due to its low ability for clonal propagation. In four populations in Niigata Prefecture, most individuals were fixed for a single homozygous genotype at all loci. Artemisia stelleriana is considered to have a flower structure suitable for self‐pollination, and it is assumed that this extremely low genetic diversity has been established through repeated self‐pollination within the population, with little gene flow between populations. Investigation of the genetic diversity and structure is necessary in the other four prefectures, where A. stelleriana is classified as an endangered species, in the future.

@article{doi1011111442198470007,
    author = "Abe, Haruno and Takeda, Kota and Hasegawa, Yoichi and Uchiyama, Kentaro and Moriguchi, Y.",
    title = "Ecological characteristics of the coastal dune plant Artemisia stelleriana, along with genetic diversity of populations at Niigata Prefecture in Japan",
    year = "2025",
    journal = "Plant Species Biology",
    abstract = "Coastal dune plants play an important role in maintaining the stability of coastal dune areas. Artemisia stelleriana Besser. is a coastal dune plant with a northern distribution, and populations are scattered and isolated in Japan due to habitat loss, leading to its classification as an endangered species in several prefectures. However, very few ecological and genetic studies of A. stelleriana have been conducted worldwide. This study was performed to investigate the self‐compatibility, flower structure, and flowering phenology, seed thalassochory potential, and clonal propagation ability of A. stelleriana, along with the genetic diversity of four populations in Niigata Prefecture. Our results showed that A. stelleriana is self‐compatible, with a flower head composed of female and hermaphrodite florets that have overlapping flowering periods. The species also exhibits a relatively short seed floating period, which leads to limited seed dispersal by sea currents, and possesses a weak clonal structure due to its low ability for clonal propagation. In four populations in Niigata Prefecture, most individuals were fixed for a single homozygous genotype at all loci. Artemisia stelleriana is considered to have a flower structure suitable for self‐pollination, and it is assumed that this extremely low genetic diversity has been established through repeated self‐pollination within the population, with little gene flow between populations. Investigation of the genetic diversity and structure is necessary in the other four prefectures, where A. stelleriana is classified as an endangered species, in the future.",
    url = "https://www.semanticscholar.org/paper/88cd908787551d365d51efc049e5f7a49a4671ee",
    doi = "10.1111/1442-1984.70007",
    is_oa = "true",
    number = "4",
    pages = "378-390",
    semanticscholar_id = "88cd908787551d365d51efc049e5f7a49a4671ee",
    volume = "40"
}

River barriers have long played a central role in diversification models of tropical regions, including the exceptionally biodiverse island Madagascar. Although their role is best understood by integrating additional factors such as elevation and the ecological niche of a species, empirical studies integrating these variables remain rare. We used restriction site-associated DNA sequencing to assess the combined effect of rivers, topography, climate and forest cover on the distributions and diversity of four Microcebus and two Avahi species (Primates, Lemuriformes) in northeastern Madagascar. We inferred population structure, gene flow and genetic diversity, and assessed the association of these ecogeographic variables and genetic differentiation using isolation-by-resistance models. Our results show that significant differences in genetic diversity and connectivity among species can be explained by species-specific responses to landscape features and phylogeographic histories. Specifically, rivers present general barriers to gene flow, but dispersal between inter-river systems is possible via high-elevation headwater regions. While this led to high connectivity and genetic diversity in M. lehilahytsara and A. laniger, gene flow among M. jonahi populations is limited by low climatic niche suitability at higher elevations. Moreover, the more restricted distributions of M. macarthurii, M. simmonsi and A. mooreorum likely resulted from refugial dynamics and sea level fluctuations leading to allopatric divergence and microendemism. Together, the findings illustrate how ecological differences among species and temporal landscape dynamics mediate the role of rivers as dispersal barriers. They also highlight the importance of prioritising river headwaters and topographically complex regions, which were shown to promote connectivity, in conservation efforts.

@article{doi101111mec70195,
    author = "van Elst, Tobias and Schüßler, Dominik and Rafamantanantsoa, Stephan M and Radriarimanga, Tahiriniaina and Rabemananjara, Naina R and Rasolofoson, David W and Randimbiharinirina, R Doménico and Hohenlohe, Paul A and Radespiel, Ute",
    title = "Species-Specific Responses to Paleoclimatic Changes and Landscape Barriers Drive Contrasting Phylogeography of Co-Distributed Lemur Species in Northeastern Madagascar.",
    year = "2025",
    journal = "Molecular ecology",
    abstract = "River barriers have long played a central role in diversification models of tropical regions, including the exceptionally biodiverse island Madagascar. Although their role is best understood by integrating additional factors such as elevation and the ecological niche of a species, empirical studies integrating these variables remain rare. We used restriction site-associated DNA sequencing to assess the combined effect of rivers, topography, climate and forest cover on the distributions and diversity of four Microcebus and two Avahi species (Primates, Lemuriformes) in northeastern Madagascar. We inferred population structure, gene flow and genetic diversity, and assessed the association of these ecogeographic variables and genetic differentiation using isolation-by-resistance models. Our results show that significant differences in genetic diversity and connectivity among species can be explained by species-specific responses to landscape features and phylogeographic histories. Specifically, rivers present general barriers to gene flow, but dispersal between inter-river systems is possible via high-elevation headwater regions. While this led to high connectivity and genetic diversity in M. lehilahytsara and A. laniger, gene flow among M. jonahi populations is limited by low climatic niche suitability at higher elevations. Moreover, the more restricted distributions of M. macarthurii, M. simmonsi and A. mooreorum likely resulted from refugial dynamics and sea level fluctuations leading to allopatric divergence and microendemism. Together, the findings illustrate how ecological differences among species and temporal landscape dynamics mediate the role of rivers as dispersal barriers. They also highlight the importance of prioritising river headwaters and topographically complex regions, which were shown to promote connectivity, in conservation efforts.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12717996/",
    doi = "10.1111/mec.70195",
    pmcid = "PMC12717996",
    pmid = "41367356"
}

Background Dispersal limitations vary among species within the same region. For some species, geographic distance is the primary constraint, while for others, environmental factors such as climate and vegetation patterns play a larger role. These landscape-driven effects are shaped by species-specific ecological traits. Despite being conceptually intuitive, landscape genetics hypotheses—such as Isolation by Distance and Isolation by Environment—remain largely underexplored in tropical regions. We conducted a comparative landscape genetics study to assess the influence of geographic and environmental landscape features on genetic differentiation in two ecologically distinct anurans species: Dendropsophus oliveirai, a diminutive treefrog that uses ponds for reproduction and larval development, and Physalaemus cuvieri, a terrestrial frog that breeds in both ponds and rain pools, depositing eggs in foam nests where embryos develop. These species co-occur in highland forest enclaves within a dry vegetation matrix across the Borborema Plateau, northeastern Brazil. Methods We sampled individuals of both species in seven highland forest enclaves to assess phylogeographic patterns and genetic variation along the steep NE-SW climatic and vegetation gradient characterizing the plateau. Additionally, we collected geographic, climatic, and vegetation data for each site. We analyzed the relationships between geographic distance, environmental variation, climatic variation, and mtDNA genetic differentiation in both species using Mantel tests and Structural Equation Modeling. Results We found lower genetic differentiation in P. cuvieri, which was primarily associated with the geographic distance among enclaves, with only weak influence of environmental variation among sampling sites. Conversely, higher genetic differentiation was detected among geographic populations of D. oliveirai, mainly driven by a combination of geographic distance, environmental heterogeneity, and past climatic variation. Conclusions The contrasting genetic structures of the two species likely result from differences in their ability to traverse dry lowland areas between mesic highland forests, with Isolation by Distance and Isolation by Environment affecting each species differently. These findings suggest that both selective and neutral mechanisms contribute to genetic variation. Our study highlights that highland forests in northeastern Brazil may harbor genetically distinct anuran populations, where gene flow is constrained not only by geographic distance but also by environmental factors, especially in diminutive species with specific reproductive needs.

@article{doi101186s1371702500625w,
    author = "de Andrade Lima, J. H. and Katzenberger, Marco and Gehara, Marcelo and Simões, P. I.",
    title = "Landscape genetics highlights species-specific ecological influences on gene flow in highland frog populations from northeastern Brazil",
    year = "2025",
    journal = "Ecological Processes",
    abstract = "Background Dispersal limitations vary among species within the same region. For some species, geographic distance is the primary constraint, while for others, environmental factors such as climate and vegetation patterns play a larger role. These landscape-driven effects are shaped by species-specific ecological traits. Despite being conceptually intuitive, landscape genetics hypotheses—such as Isolation by Distance and Isolation by Environment—remain largely underexplored in tropical regions. We conducted a comparative landscape genetics study to assess the influence of geographic and environmental landscape features on genetic differentiation in two ecologically distinct anurans species: Dendropsophus oliveirai, a diminutive treefrog that uses ponds for reproduction and larval development, and Physalaemus cuvieri, a terrestrial frog that breeds in both ponds and rain pools, depositing eggs in foam nests where embryos develop. These species co-occur in highland forest enclaves within a dry vegetation matrix across the Borborema Plateau, northeastern Brazil. Methods We sampled individuals of both species in seven highland forest enclaves to assess phylogeographic patterns and genetic variation along the steep NE-SW climatic and vegetation gradient characterizing the plateau. Additionally, we collected geographic, climatic, and vegetation data for each site. We analyzed the relationships between geographic distance, environmental variation, climatic variation, and mtDNA genetic differentiation in both species using Mantel tests and Structural Equation Modeling. Results We found lower genetic differentiation in P. cuvieri, which was primarily associated with the geographic distance among enclaves, with only weak influence of environmental variation among sampling sites. Conversely, higher genetic differentiation was detected among geographic populations of D. oliveirai, mainly driven by a combination of geographic distance, environmental heterogeneity, and past climatic variation. Conclusions The contrasting genetic structures of the two species likely result from differences in their ability to traverse dry lowland areas between mesic highland forests, with Isolation by Distance and Isolation by Environment affecting each species differently. These findings suggest that both selective and neutral mechanisms contribute to genetic variation. Our study highlights that highland forests in northeastern Brazil may harbor genetically distinct anuran populations, where gene flow is constrained not only by geographic distance but also by environmental factors, especially in diminutive species with specific reproductive needs.",
    url = "https://www.semanticscholar.org/paper/f460792e7975888d2784e16cddda67a6c21069f1",
    doi = "10.1186/s13717-025-00625-w",
    is_oa = "true",
    number = "1",
    semanticscholar_id = "f460792e7975888d2784e16cddda67a6c21069f1",
    volume = "14"
}

IAP proteins play central roles in regulating apoptosis and diverse cellular processes, influencing cancer biology, or stress resistance in economically important species, highlighting their major biomedical and ecological relevance. Despite this importance, IAP evolutionary diversity and history remain largely unexplored. Here, we present a large-scale comparative analysis of 2,843 IAP proteins from 312 species spanning all major animal lineages, revealing striking variation in IAP repertoire size and exceptional architectural diversity. We show that IAP expansion has repeatedly emerged through lineage-specific duplication events, seemingly shaped by different duplication dynamics with more recent gene family expansions in arthropods compared to molluscs and chordates. Expression data show that IAP expansion supports distinct strategies. Bivalves and gastropods mobilize multiple IAP subfamilies in response to biotic and abiotic stress, whereas aphids exhibit differential IAP expression associated with polyphenism. These contrasting patterns indicate that heterogeneous selective pressures have recurrently reshaped IAP repertoires, promoting lineage- and species-specific functional diversification. Despite this diversification, phylogenetic analyses reveal the maintenance of a core set of three IAP types. Survivin/Deterin-like and Bruce-like IAPs emerged early in metazoans and remained structurally conserved, although Bruce-like IAPs were independently lost in chelicerates, most nematodes and some hemipteran insects. RING-containing IAPs also originated early but followed more dynamic evolutionary trajectories, being lost in nematodes and platyhelminths while expanding in other lineages through domain acquisition (e.g., gnathostomes) or repeated domain duplication and loss (e.g., molluscs and insects). Our findings establish a comprehensive evolutionary framework for metazoan IAPs, linking lineage-specific diversification to structural innovation and functional specialization.

@article{doi101093molbevmsag078,
    author = "Ribeiro Lopes, Mélanie and Parisot, Nicolas and Peignier, Sergio and Renoz, François and Baa-Puyoulet, Patrice and Jousselin, Emmanuelle and Charles, Hubert and Callaerts, Patrick and Brochier-Armanet, Céline and Calevro, Federica",
    title = "Evolutionary trajectories, early diversification and species-specific amplification of the metazoan Inhibitor of Apoptosis (IAP) repertoire.",
    year = "2026",
    journal = "Molecular biology and evolution",
    abstract = "IAP proteins play central roles in regulating apoptosis and diverse cellular processes, influencing cancer biology, or stress resistance in economically important species, highlighting their major biomedical and ecological relevance. Despite this importance, IAP evolutionary diversity and history remain largely unexplored. Here, we present a large-scale comparative analysis of 2,843 IAP proteins from 312 species spanning all major animal lineages, revealing striking variation in IAP repertoire size and exceptional architectural diversity. We show that IAP expansion has repeatedly emerged through lineage-specific duplication events, seemingly shaped by different duplication dynamics with more recent gene family expansions in arthropods compared to molluscs and chordates. Expression data show that IAP expansion supports distinct strategies. Bivalves and gastropods mobilize multiple IAP subfamilies in response to biotic and abiotic stress, whereas aphids exhibit differential IAP expression associated with polyphenism. These contrasting patterns indicate that heterogeneous selective pressures have recurrently reshaped IAP repertoires, promoting lineage- and species-specific functional diversification. Despite this diversification, phylogenetic analyses reveal the maintenance of a core set of three IAP types. Survivin/Deterin-like and Bruce-like IAPs emerged early in metazoans and remained structurally conserved, although Bruce-like IAPs were independently lost in chelicerates, most nematodes and some hemipteran insects. RING-containing IAPs also originated early but followed more dynamic evolutionary trajectories, being lost in nematodes and platyhelminths while expanding in other lineages through domain acquisition (e.g., gnathostomes) or repeated domain duplication and loss (e.g., molluscs and insects). Our findings establish a comprehensive evolutionary framework for metazoan IAPs, linking lineage-specific diversification to structural innovation and functional specialization.",
    url = "https://pubmed.ncbi.nlm.nih.gov/41876750/",
    doi = "10.1093/molbev/msag078",
    pmid = "41876750"
}

Abstract. Lekitoo MN, Lekitoo T, Santoso B, Saragih EW, Yoku O, Hariadi BT, Iyai DA, Sonbait LY. 2026. Forage species diversity and composition, and carrying capacity of rangelands in Teluk Wondama Regency, West Papua, Indonesia. Biodiversitas 27 (1): d270111. https://doi.org/10.13057/biodiv/d270111. Rangelands and natural pastures serve as the backbone of livestock feed. However, there is limited empirical data on their productivity and capacity to sustain livestock populations in lesser-known regions, such as Papua. The study aims to assess the botanical diversity and composition of forage in natural rangeland in Teluk Wondama Regency, West Papua, Indonesia, and to evaluate its carrying capacity. Botanical sampling was conducted by establishing 30 sample plots measuring 1×1 m2 in areas of 64 ha within the Warayaro natural rangelands. Forage productivity was estimated based on botanical composition, fresh forage, dry matter, and total digestible nutrients. The findings reveal that the rangeland in Warayaro is a heterogeneous pasture comprising 5 types of fodder, including 4 grasses and 1 legume species. Non-native species from 3 families dominated the pasture, namely Paspalum dilatatum, followed by Paspalum conjugatum, Centrosema pubescens, Eleusine indica, and Cyperus rotundus. The botanical composition consisted of 86.7% grasses and 13.3% legumes. Average forage yield is 2.0 t FM, 0.4 t ha-1 and 1.02 t ha-1 TDN. The existing Warayaro forage has a carrying capacity for cattle of 0.4 AU ha-1 yr-1 (FM), 0.3 AU ha-1 yr-1 (DM) and 0.8 AU ha-1 yr-1 (TDN). The Warayaro natural pasture has low production potential (264.7 kg TDN per 100 kg of livestock body weight) and moderate nutritional quality, with a protein content of only 11.2%. The Warayaro pasture is more suitable for growing young stock to reach a body weight of 182 kg. The carrying capacity of the rangeland for cattle and goat is 32 head yr-1 is 320 head yr-1, respectively. Key ecological recommendations include increasing the proportion of legumes through reseeding, implementing rotational grazing, and monitoring and controlling Cyperus rotundus to prevent competitive exclusion of forage species.

@article{doi1013057biodivd270111,
    author = "Lekitoo, M. and Lekitoo, Teddy and Santoso, Budi and Saragih, E. W. and Yoku, O. and Hariadi, Bambang and Iyai, D. and Sonbait, L. Y.",
    title = "Forage species diversity and composition, and carrying capacity of rangelands in Teluk Wondama Regency, West Papua, Indonesia",
    year = "2026",
    journal = "Biodiversitas Journal of Biological Diversity",
    abstract = "Abstract. Lekitoo MN, Lekitoo T, Santoso B, Saragih EW, Yoku O, Hariadi BT, Iyai DA, Sonbait LY. 2026. Forage species diversity and composition, and carrying capacity of rangelands in Teluk Wondama Regency, West Papua, Indonesia. Biodiversitas 27 (1): d270111. https://doi.org/10.13057/biodiv/d270111. Rangelands and natural pastures serve as the backbone of livestock feed. However, there is limited empirical data on their productivity and capacity to sustain livestock populations in lesser-known regions, such as Papua. The study aims to assess the botanical diversity and composition of forage in natural rangeland in Teluk Wondama Regency, West Papua, Indonesia, and to evaluate its carrying capacity. Botanical sampling was conducted by establishing 30 sample plots measuring 1×1 m2 in areas of 64 ha within the Warayaro natural rangelands. Forage productivity was estimated based on botanical composition, fresh forage, dry matter, and total digestible nutrients. The findings reveal that the rangeland in Warayaro is a heterogeneous pasture comprising 5 types of fodder, including 4 grasses and 1 legume species. Non-native species from 3 families dominated the pasture, namely Paspalum dilatatum, followed by Paspalum conjugatum, Centrosema pubescens, Eleusine indica, and Cyperus rotundus. The botanical composition consisted of 86.7\% grasses and 13.3\% legumes. Average forage yield is 2.0 t FM, 0.4 t ha-1 and 1.02 t ha-1 TDN. The existing Warayaro forage has a carrying capacity for cattle of 0.4 AU ha-1 yr-1 (FM), 0.3 AU ha-1 yr-1 (DM) and 0.8 AU ha-1 yr-1 (TDN). The Warayaro natural pasture has low production potential (264.7 kg TDN per 100 kg of livestock body weight) and moderate nutritional quality, with a protein content of only 11.2\%. The Warayaro pasture is more suitable for growing young stock to reach a body weight of 182 kg. The carrying capacity of the rangeland for cattle and goat is 32 head yr-1 is 320 head yr-1, respectively. Key ecological recommendations include increasing the proportion of legumes through reseeding, implementing rotational grazing, and monitoring and controlling Cyperus rotundus to prevent competitive exclusion of forage species.",
    url = "https://www.semanticscholar.org/paper/0afa171ff85ce45d7705d06f60e2776cea25679b",
    doi = "10.13057/biodiv/d270111",
    is_oa = "true",
    number = "1",
    semanticscholar_id = "0afa171ff85ce45d7705d06f60e2776cea25679b",
    volume = "27"
}

Studying intraspecific differentiation in closely related species is essential to clarify the phylogenetic relationships and mechanisms of early stage speciation, particularly in evolutionarily young lineages affected by human-driven population declines. The endangered saker falcon (Falco cherrug), with its ambiguous phylogenetic links to the gyrfalcon (F. rusticolus), exemplifies this scenario. This study presents a comprehensive genetic analysis of F. cherrug and F. rusticolus using mtDNA markers and microsatellite loci, focusing on the diversity of southern Siberian saker falcon populations. The genotyping results for these populations were correlated with phenotypic data obtained from long-term monitoring (1999–2021). Our findings provide novel insights into the current subspecific differentiation and the remnants of a nascent subspecies structure that existed before the recent demographic collapse. Furthermore, our results support the hypothesis of the gyrfalcon’s origin as a descendant species of the Asian saker falcon, i.e., an evolutionarily young lineage undergoing divergence. Our data contribute to the understanding of the Hierofalco evolutionary history, particularly through the analysis of heterogeneous mutation rates among mitochondrial haplogroups. This study underscores the critical importance of conservation efforts for wild endangered populations through long-term monitoring integrated with combined genetic approaches.

@article{doi103390d18010050,
    author = "Rozhkova, D. and Shnayder, E. P. and Tambovtseva, V. and Karyakin, I. and Blekhman, A. V. and Lazebny, Oleg E and Sorokina, S. and Zinevich, L. and Kulikov, A. M.",
    title = "Evolutionary Relationships and Genetic Diversity in the Southern Siberian Populations of the Saker Falcon (Falco cherrug), a Young and Endangered Species",
    year = "2026",
    journal = "Diversity",
    abstract = "Studying intraspecific differentiation in closely related species is essential to clarify the phylogenetic relationships and mechanisms of early stage speciation, particularly in evolutionarily young lineages affected by human-driven population declines. The endangered saker falcon (Falco cherrug), with its ambiguous phylogenetic links to the gyrfalcon (F. rusticolus), exemplifies this scenario. This study presents a comprehensive genetic analysis of F. cherrug and F. rusticolus using mtDNA markers and microsatellite loci, focusing on the diversity of southern Siberian saker falcon populations. The genotyping results for these populations were correlated with phenotypic data obtained from long-term monitoring (1999–2021). Our findings provide novel insights into the current subspecific differentiation and the remnants of a nascent subspecies structure that existed before the recent demographic collapse. Furthermore, our results support the hypothesis of the gyrfalcon’s origin as a descendant species of the Asian saker falcon, i.e., an evolutionarily young lineage undergoing divergence. Our data contribute to the understanding of the Hierofalco evolutionary history, particularly through the analysis of heterogeneous mutation rates among mitochondrial haplogroups. This study underscores the critical importance of conservation efforts for wild endangered populations through long-term monitoring integrated with combined genetic approaches.",
    url = "https://www.semanticscholar.org/paper/e42251a24980f0c4c7467a2384f68f00f9e274fd",
    doi = "10.3390/d18010050",
    is_oa = "true",
    number = "1",
    pages = "50",
    semanticscholar_id = "e42251a24980f0c4c7467a2384f68f00f9e274fd",
    volume = "18"
}

This study investigates plant species diversity, regeneration patterns, and the ecological drivers influencing endangered plant species in the Than Sa–Phuong Hoang Nature Reserve, Thai Nguyen Province, Vietnam. Although tropical forest ecosystems in Southeast Asia are known for their high biodiversity, there is still a lack of site-specific studies that integrate species diversity, regeneration dynamics, and environmental drivers at the reserve scale. A total of 15 standard plots (20 × 50 m) were established across three main forest types (limestone forests, soil mountain forests, and transitional forests) to assess species composition, community structure, and regeneration patterns. Multivariate analyses, including principal component analysis (PCA) and cluster analysis, were applied to identify key ecological factors shaping species distribution and regeneration. The results recorded 1234 plant species belonging to 171 families, confirming the high biodiversity of the study area. Regeneration capacity differed significantly among forest types and was strongly influenced by environmental variables such as canopy cover, soil moisture, topography, and human disturbance. Multivariate results revealed clear ecological differentiation among forest types, highlighting the role of environmental filtering in structuring plant communities. The three target species (Curculigo orchioides Gaertn, Parashorea chinensis, and Paphiopedilum hirsutissimum Stein) exhibited strong dependence on stable microhabitat conditions and showed limited regeneration under disturbed environments, indicating high sensitivity to ecological changes and anthropogenic pressure. This study provides new insights into species–environment relationships at a local scale and highlights key ecological drivers of endangered plant distribution and regeneration, contributing to more effective conservation planning and biodiversity management in tropical forest ecosystems.

@article{doi103390d18040228,
    author = "Dang, Thi Thai Ha and Hoang, Van Hung and Nguyen, C. and Do, V.",
    title = "Diversity Conservation Status, and Ecological Characteristics of Endangered Plant Species in Than Sa–Phuong Hoang Nature Reserve, Thai Nguyen Province, Vietnam",
    year = "2026",
    journal = "Diversity",
    abstract = "This study investigates plant species diversity, regeneration patterns, and the ecological drivers influencing endangered plant species in the Than Sa–Phuong Hoang Nature Reserve, Thai Nguyen Province, Vietnam. Although tropical forest ecosystems in Southeast Asia are known for their high biodiversity, there is still a lack of site-specific studies that integrate species diversity, regeneration dynamics, and environmental drivers at the reserve scale. A total of 15 standard plots (20 × 50 m) were established across three main forest types (limestone forests, soil mountain forests, and transitional forests) to assess species composition, community structure, and regeneration patterns. Multivariate analyses, including principal component analysis (PCA) and cluster analysis, were applied to identify key ecological factors shaping species distribution and regeneration. The results recorded 1234 plant species belonging to 171 families, confirming the high biodiversity of the study area. Regeneration capacity differed significantly among forest types and was strongly influenced by environmental variables such as canopy cover, soil moisture, topography, and human disturbance. Multivariate results revealed clear ecological differentiation among forest types, highlighting the role of environmental filtering in structuring plant communities. The three target species (Curculigo orchioides Gaertn, Parashorea chinensis, and Paphiopedilum hirsutissimum Stein) exhibited strong dependence on stable microhabitat conditions and showed limited regeneration under disturbed environments, indicating high sensitivity to ecological changes and anthropogenic pressure. This study provides new insights into species–environment relationships at a local scale and highlights key ecological drivers of endangered plant distribution and regeneration, contributing to more effective conservation planning and biodiversity management in tropical forest ecosystems.",
    url = "https://www.semanticscholar.org/paper/3e08c13a35200826c71f993ab4fcf48a8e31ea05",
    doi = "10.3390/d18040228",
    is_oa = "true",
    number = "4",
    pages = "228",
    semanticscholar_id = "3e08c13a35200826c71f993ab4fcf48a8e31ea05",
    volume = "18"
}

DNA methylation constitutes a primary layer of epigenetic regulation in plants, operating across three sequence contexts (CG, CHG, and CHH) through distinct enzymatic pathways. Over the past fifteen years, accumulating evidence has shown that DNA methylation varies substantially among individuals and populations of wild plants, sometimes independently of underlying genetic polymorphism. This variation can influence gene expression, transposable element activity, and phenotypic traits relevant to ecological adaptation. Population epigenetics, the study of methylation variation at the population scale, has matured from initial surveys using methylation-sensitive amplified fragment length polymorphism (MS-AFLP) into a discipline increasingly reliant on reduced-representation bisulfite sequencing (epiGBS, bsRADseq), whole-genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), and direct long-read detection by nanopore sequencing. These methodological advances are opening population epigenetics to non-model organisms across the full breadth of the plant phylogeny, from angiosperms and gymnosperms to ferns and bryophytes. We cover (i) the molecular machinery underlying plant DNA methylation, including the debated status of N6-methyladenine (6mA); (ii) empirical evidence for natural epigenetic variation in plant populations, spanning clonal, invasive, and outcrossing species; (iii) the methodological toolkit available for population-scale methylation profiling, with emphasis on approaches suitable for non-model taxa; and (iv) the ecological and evolutionary significance of population epigenetic variation, including transgenerational inheritance, stress memory, epigenetic clocks, conservation applications, and the emerging integration of epigenetics into the extended evolutionary synthesis. We identify critical knowledge gaps, particularly the near-complete absence of population-level epigenetic data for bryophytes, ferns, and lycophytes, and outline priorities for future research.

@article{doi103390d18050259,
    author = "Sawicki, Jakub and Czochór, Wiktoria and Garbowska, Aniela and Koczwara, Kamil and Przyborowski, Jerzy Andrzej and Pupek, Natan and Sulima, P. and Szablińska, Joanna and Szczecińska, M.",
    title = "Epigenetic Variation in Plant Populations: DNA Methylation as a Driver of Phenotypic Diversity and Adaptation",
    year = "2026",
    journal = "Diversity",
    abstract = "DNA methylation constitutes a primary layer of epigenetic regulation in plants, operating across three sequence contexts (CG, CHG, and CHH) through distinct enzymatic pathways. Over the past fifteen years, accumulating evidence has shown that DNA methylation varies substantially among individuals and populations of wild plants, sometimes independently of underlying genetic polymorphism. This variation can influence gene expression, transposable element activity, and phenotypic traits relevant to ecological adaptation. Population epigenetics, the study of methylation variation at the population scale, has matured from initial surveys using methylation-sensitive amplified fragment length polymorphism (MS-AFLP) into a discipline increasingly reliant on reduced-representation bisulfite sequencing (epiGBS, bsRADseq), whole-genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), and direct long-read detection by nanopore sequencing. These methodological advances are opening population epigenetics to non-model organisms across the full breadth of the plant phylogeny, from angiosperms and gymnosperms to ferns and bryophytes. We cover (i) the molecular machinery underlying plant DNA methylation, including the debated status of N6-methyladenine (6mA); (ii) empirical evidence for natural epigenetic variation in plant populations, spanning clonal, invasive, and outcrossing species; (iii) the methodological toolkit available for population-scale methylation profiling, with emphasis on approaches suitable for non-model taxa; and (iv) the ecological and evolutionary significance of population epigenetic variation, including transgenerational inheritance, stress memory, epigenetic clocks, conservation applications, and the emerging integration of epigenetics into the extended evolutionary synthesis. We identify critical knowledge gaps, particularly the near-complete absence of population-level epigenetic data for bryophytes, ferns, and lycophytes, and outline priorities for future research.",
    url = "https://www.semanticscholar.org/paper/73586a28532bd4c93909ae73eafa8aa933538cfc",
    doi = "10.3390/d18050259",
    is_oa = "true",
    number = "5",
    pages = "259",
    semanticscholar_id = "73586a28532bd4c93909ae73eafa8aa933538cfc",
    volume = "18"
}